1. mzR
  2. man
  3. peaks.Rd
Browse code

refactor: header always returns a `data.frame` (PR #253)

- Fix header for pwiz backend to always return a `data.frame`.
- Update documentation.

jorainer authored on 25/11/2021 08:27:02
Showing 1 changed files
man/peaks.Rd
History View file @ ee9c964e8f
... ... 
@@ -98,7 +98,7 @@
98 98 
   provided (i.e all spectra in the oject are retured). \code{peaksCount}
99 99 
   will return a numeric of length \code{n}.
100 100
101 
-  The \code{\link{header}} function returns a list containing
101 
+  The \code{\link{header}} function returns a \code{data.frame} containing
102 102 
   \code{seqNum}, \code{acquisitionNum}, \code{msLevel},
103 103 
   \code{peaksCount}, \code{totIonCurrent}, \code{retentionTime} (in
104 104 
   seconds), \code{basePeakMZ}, \code{basePeakIntensity},
Browse code

Remove Ramp backend with dependencies

jorainer authored on 20/09/2021 12:19:56
Showing 1 changed files
man/peaks.Rd
History View file @ e3f79ff5f7
... ... 
@@ -5,33 +5,23 @@
5 5 
 \alias{peaksCount}
6 6 
 \alias{get3Dmap}
7 7
8 
-\alias{header,mzRramp,missing-method}
9 
-\alias{header,mzRramp,numeric-method}
10 8 
 \alias{header,mzRpwiz,missing-method}
11 9 
 \alias{header,mzRpwiz,numeric-method}
12 10 
 \alias{header,mzRnetCDF,missing-method}
13 11 
 \alias{header,mzRnetCDF,numeric-method}
14 12
15 
-\alias{peaksCount,mzRramp,missing-method}
16 
-\alias{peaksCount,mzRramp,numeric-method}
17 13 
 \alias{peaksCount,mzRpwiz,missing-method}
18 14 
 \alias{peaksCount,mzRpwiz,numeric-method}
19 
-\alias{peaks,mzRramp-method}
20 
-\alias{spectra,mzRramp-method}
21 15 
 \alias{peaks,mzRpwiz-method}
22 16 
 \alias{spectra,mzRpwiz-method}
23 17 
 \alias{peaks,mzRnetCDF-method}
24 18 
 \alias{spectra,mzRnetCDF-method}
25 19
26 
-\alias{get3Dmap,mzRramp-method}
27 20 
 \alias{get3Dmap,mzRpwiz-method}
28 21
29 22 
 \alias{chromatogram,mzRpwiz-method}
30 23 
 \alias{chromatogramHeader,mzRpwiz-method}
31 24 
 \alias{chromatograms,mzRpwiz-method}
32 
-\alias{chromatogram,mzRramp-method}
33 
-\alias{chromatogramHeader,mzRramp-method}
34 
-\alias{chromatograms,mzRramp-method}
35 25 
 \alias{chromatogram,mzRnetCDF-method}
36 26 
 \alias{chromatogramHeader,mzRnetCDF-method}
37 27 
 \alias{chromatograms,mzRnetCDF-method}
... ... 
@@ -54,11 +44,9 @@
54 44 
  peaksCount(object, scans, ...)
55 45
56 46 
  \S4method{peaks}{mzRpwiz}(object, scans)
57 
- \S4method{peaks}{mzRramp}(object, scans)
58 47 
  \S4method{peaks}{mzRnetCDF}(object, scans)
59 48
60 49 
  \S4method{spectra}{mzRpwiz}(object, scans)   ## same as peaks
61 
- \S4method{spectra}{mzRramp}(object, scans)
62 50 
  \S4method{spectra}{mzRnetCDF}(object, scans)
63 51
64 52 
  get3Dmap(object, scans, lowMz, highMz, resMz, ...)
Browse code

refactor: rewrite the peak extraction function for pwiz

- Rewrite the C++ code for peak data extraction with the pwiz backend.
- Fix unit tests.

jorainer authored on 26/09/2019 10:09:04
Showing 1 changed files
man/peaks.Rd
History View file @ 5bcb9d2bd7
... ... 
@@ -128,7 +128,7 @@
128 128 
   \code{isolationWindowUpperOffset}, \code{scanWindowLowerLimit} and
129 129 
   \code{scanWindowUpperLimit}. If multiple scans are queried, a
130 130 
   \code{data.frame} is returned with the scans reported along the
131 
-  rows.
131 
+  rows. For missing or not defined spectrum variables \code{NA} is reported.
132 132
133 133 
   The \code{get3Dmap} function performs a simple resampling between
134 134 
   \code{lowMz} and \code{highMz} with \code{reMz} resolution. A matrix
Browse code

Add scanWindowLowerLimit and scanWindowUpperLimit to header

- Add scanWindowLowerLimit and scanWindowUpperLimit variables.
- Export scanWindowLowerLimit and scanWindowUpperLimit to mzML (issue #202).
- Update and amend documentation and unit tests accordingly.

jorainer authored on 23/08/2019 14:02:46
Showing 1 changed files
man/peaks.Rd
History View file @ 52172a4d17
... ... 
@@ -124,8 +124,9 @@
124 124 
   or profile mode; only for pwiz backend), \code{injectionTime} (ion
125 125 
   injection time, in milliseconds), \code{ionMobilityDriftTime} (in
126 126 
   milliseconds), \code{isolationWindowTargetMZ},
127 
-  \code{isolationWindowLowerOffset} and
128 
-  \code{isolationWindowUpperOffset}. If multiple scans are queried, a
127 
+  \code{isolationWindowLowerOffset},
128 
+  \code{isolationWindowUpperOffset}, \code{scanWindowLowerLimit} and
129 
+  \code{scanWindowUpperLimit}. If multiple scans are queried, a
129 130 
   \code{data.frame} is returned with the scans reported along the
130 131 
   rows.
131 132
Browse code

Add isolationWindowTargetMZ column to header

- Extract isolation window from mzML files (issue #193): data.frame returned by
jeader gains columns "isolationWindowTargetMZ", "isolationWindowLowerOffset"
and "isolationWindowUpperOffset" enabling SWATH data analysis.
- Adapt documentation and unit tests.

jotsetung authored on 03/04/2019 09:40:16
Showing 1 changed files
man/peaks.Rd
History View file @ 2edb9032d0
... ... 
@@ -122,8 +122,10 @@
122 122 
   \code{filterString}, \code{spectrumId}, \code{centroided}
123 123 
   (\code{logical} whether the data of the spectrum is in centroid mode
124 124 
   or profile mode; only for pwiz backend), \code{injectionTime} (ion
125 
-  injection time, in milliseconds) and \code{ionMobilityDriftTime} (in
126 
-  milliseconds). If multiple scans are queried, a
125 
+  injection time, in milliseconds), \code{ionMobilityDriftTime} (in
126 
+  milliseconds), \code{isolationWindowTargetMZ},
127 
+  \code{isolationWindowLowerOffset} and
128 
+  \code{isolationWindowUpperOffset}. If multiple scans are queried, a
127 129 
   \code{data.frame} is returned with the scans reported along the
128 130 
   rows.
129 131
Browse code

Add ionMobilityDriftTime to header (issue #44)

- Extract the ion mobility drift time from mzML files (if available).
- Ensure that ion injection time is always reported in milliseconds.
- Update unit tests and documentation.

jotsetung authored on 30/08/2018 09:25:03
Showing 1 changed files
man/peaks.Rd
History View file @ 817d14206b
... ... 
@@ -119,10 +119,11 @@
119 119 
   \code{precursorCharge}, \code{precursorIntensity},
120 120 
   \code{mergedScan}, \code{mergedResultScanNum},
121 121 
   \code{mergedResultStartScanNum}, \code{mergedResultEndScanNum},
122 
-  \code{spectrumId}, \code{centroided} (\code{logical} whether the data
123 
-  of the spectrum is in centroid mode or profile mode; only for pwiz
124 
-  backend) and \code{injectionTime} (ion injection time, in milliseconds)
125 
-  when available in the original file. If multiple scans are queried, a
122 
+  \code{filterString}, \code{spectrumId}, \code{centroided}
123 
+  (\code{logical} whether the data of the spectrum is in centroid mode
124 
+  or profile mode; only for pwiz backend), \code{injectionTime} (ion
125 
+  injection time, in milliseconds) and \code{ionMobilityDriftTime} (in
126 
+  milliseconds). If multiple scans are queried, a
126 127 
   \code{data.frame} is returned with the scans reported along the
127 128 
   rows.
128 129
Browse code

Add .hasChromatograms function (issue #164)

- Add the .hasChromatograms function.
- Add chromatogram, chromatograms and chromatogramHeader methods for the ramp
and netCDF backends.
- Add related unit tests.

jotsetung authored on 16/05/2018 12:53:42
Showing 1 changed files
man/peaks.Rd
History View file @ b61d82bf47
... ... 
@@ -29,6 +29,12 @@
29 29 
 \alias{chromatogram,mzRpwiz-method}
30 30 
 \alias{chromatogramHeader,mzRpwiz-method}
31 31 
 \alias{chromatograms,mzRpwiz-method}
32 
+\alias{chromatogram,mzRramp-method}
33 
+\alias{chromatogramHeader,mzRramp-method}
34 
+\alias{chromatograms,mzRramp-method}
35 
+\alias{chromatogram,mzRnetCDF-method}
36 
+\alias{chromatogramHeader,mzRnetCDF-method}
37 
+\alias{chromatograms,mzRnetCDF-method}
32 38 
 \alias{tic,mzRpwiz-method}
33 39 
 \alias{nChrom}
34 40 
 \alias{chromatogram}
Browse code

Document missing chrom argument for chromatogram(s)

Sebastian Gibb authored on 29/04/2018 07:53:05
Showing 1 changed files
man/peaks.Rd
History View file @ 3c1139ba49
... ... 
@@ -57,9 +57,9 @@
57 57
58 58 
  get3Dmap(object, scans, lowMz, highMz, resMz, ...)
59 59
60 
- chromatogram(object, ...)
60 
+ \S4method{chromatogram}{mzRpwiz}(object, chrom)
61 61
62 
- chromatograms(object, ...) ## same as chromatogram
62 
+ \S4method{chromatograms}{mzRpwiz}(object, chrom)  ## same as chromatogram
63 63
64 64 
  \S4method{chromatogramHeader}{mzRpwiz}(object, chrom)
65 65
... ... 
@@ -84,7 +84,8 @@
84 84 
   \item{resMz}{a \code{numeric} defining the m/z resolution.}
85 85
86 86 
   \item{chrom}{
87 
-    For \code{chromatogramHeader}: \code{numeric} specifying the index
87 
+    For \code{chromatogram}, \code{chromatograms} and
88 
+    \code{chromatogramHeader}: \code{numeric} specifying the index
88 89 
     of the chromatograms to be extracted from the file. If omitted, data
89 90 
     for all chromatograms is returned.
90 91 
   }
Browse code

Ensure ion_injection_time is returned and saved in milliseconds

- Related to issue #151.

jotsetung authored on 23/03/2018 13:15:47
Showing 1 changed files
man/peaks.Rd
History View file @ 8a535503d4
... ... 
@@ -114,7 +114,7 @@
114 114 
   \code{mergedResultStartScanNum}, \code{mergedResultEndScanNum},
115 115 
   \code{spectrumId}, \code{centroided} (\code{logical} whether the data
116 116 
   of the spectrum is in centroid mode or profile mode; only for pwiz
117 
-  backend) and \code{injectionTime} (ion injection time, in seconds)
117 
+  backend) and \code{injectionTime} (ion injection time, in milliseconds)
118 118 
   when available in the original file. If multiple scans are queried, a
119 119 
   \code{data.frame} is returned with the scans reported along the
120 120 
   rows.
Browse code

Read/write centroiding information from and to files

- Read centroiding information from mzML/mzXML files and write it also to these
file types (only supported on pwiz backend).
- ncdf and ramp return centroided=NA.
- Update relevant documentation and unit tests.

jotsetung authored on 23/03/2018 05:37:29
Showing 1 changed files
man/peaks.Rd
History View file @ a4b3e08fd9
... ... 
@@ -112,9 +112,10 @@
112 112 
   \code{precursorCharge}, \code{precursorIntensity},
113 113 
   \code{mergedScan}, \code{mergedResultScanNum},
114 114 
   \code{mergedResultStartScanNum}, \code{mergedResultEndScanNum},
115 
-  \code{spectrumId} and
116 
-  \code{injectionTime} (ion injection time, in seconds) when available
117 
-  in the original file. If multiple scans are queried, a
115 
+  \code{spectrumId}, \code{centroided} (\code{logical} whether the data
116 
+  of the spectrum is in centroid mode or profile mode; only for pwiz
117 
+  backend) and \code{injectionTime} (ion injection time, in seconds)
118 
+  when available in the original file. If multiple scans are queried, a
118 119 
   \code{data.frame} is returned with the scans reported along the
119 120 
   rows.
120 121
Browse code

Add chromatogramHeader method

- Add a chromatogramHeader method to extract chromatogram header information
from an mzML file (issue #141).

jotsetung authored on 11/12/2017 09:26:45
Showing 1 changed files
man/peaks.Rd
History View file @ 3555a9aa15
... ... 
@@ -27,10 +27,12 @@
27 27 
 \alias{get3Dmap,mzRpwiz-method}
28 28
29 29 
 \alias{chromatogram,mzRpwiz-method}
30 
+\alias{chromatogramHeader,mzRpwiz-method}
30 31 
 \alias{chromatograms,mzRpwiz-method}
31 32 
 \alias{tic,mzRpwiz-method}
32 33 
 \alias{nChrom}
33 34 
 \alias{chromatogram}
35 
+\alias{chromatogramHeader}
34 36 
 \alias{chromatograms}
35 37 
 \alias{tic}
36 38
... ... 
@@ -59,6 +61,8 @@
59 61
60 62 
  chromatograms(object, ...) ## same as chromatogram
61 63
64 
+ \S4method{chromatogramHeader}{mzRpwiz}(object, chrom)
65 
+
62 66 
  tic(object, ...)
63 67
64 68 
  nChrom(object)
... ... 
@@ -78,6 +82,12 @@
78 82 
     returned.}
79 83
80 84 
   \item{resMz}{a \code{numeric} defining the m/z resolution.}
85 
+
86 
+  \item{chrom}{
87 
+    For \code{chromatogramHeader}: \code{numeric} specifying the index
88 
+    of the chromatograms to be extracted from the file. If omitted, data
89 
+    for all chromatograms is returned.
90 
+  }
81 91
82 92 
   \item{...}{Other arguments. A \code{scan} parameter can be passed to
83 93 
     \code{peaks}.}  }
... ... 
@@ -128,6 +138,23 @@
128 138 
   The \code{nChrom} function returns the number of chromatograms,
129 139 
   including the total ion chromatogram.
130 140
141 
+  The \code{chromatogramHeader} returns (similar to the \code{header}
142 
+  function for spectra) a \code{data.frame} with metadata information
143 
+  for the individual chromatograms. The \code{data.frame} has the
144 
+  columns: \code{"chromatogramId"} (the ID of the chromatogram as
145 
+  specified in the file), \code{"chromatogramIndex"} (the index of the
146 
+  chromatogram within the file), \code{"polarity"} (the polarity for the
147 
+  chromatogram, 0 for negative, +1 for positive and -1 for not set),
148 
+  \code{"precursorIsolationWindowTargetMZ"} (the isolation window m/z of
149 
+  the precursor), \code{"precursorIsolationWindowLowerOffset"},
150 
+  \code{"precursorIsolationWindowUpperOffset"} (lower and upper offset
151 
+  for the isolation window m/z), \code{"precursorCollisionEnergy"}
152 
+  (collision energy),
153 
+  \code{"productIsolationWindowTargetMZ"},
154 
+  \code{"productIsolationWindowLowerOffset"} and
155 
+  \code{"productIsolationWindowUpperOffset"} (definition of the m/z
156 
+  isolation window for the product).
157 
+
131 158 
   Note that access to chromatograms is only supported in the \code{pwiz}
132 159 
   backend.
133 160
... ... 
@@ -202,4 +229,8 @@
202 229 
  head(tic(x))
203 230 
  head(chromatogram(x, 1L)) ## same as tic(x)
204 231 
  str(chromatogram(x, 10:12))
232 
+
233 
+ ## get the header information for the chromatograms
234 
+ ch <- chromatogramHeader(x)
235 
+ head(ch)
205 236 
 }
Browse code

Modify peaks example to avoid long log termination on travis

Sebastian Gibb authored on 24/11/2017 12:26:47
Showing 1 changed files
man/peaks.Rd
History View file @ 244d374bbb
... ... 
@@ -191,8 +191,8 @@
191 191 
  head(chromatogram(x, 1L)) ## same as tic(x)
192 192 
  str(chromatogram(x)) ## as a list
193 193
194 
- peaks(x) ## extract all peak information
195 
- peaks(x, scan=4) ## extract just peaks from the 4th scan
194 
+ p <- peaks(x) ## extract all peak information
195 
+ head(peaks(x, scan=4)) ## extract just peaks from the 4th scan
196 196
197 197 
  ## An MRM experiment
198 198 
  f <- proteomics(full.names = TRUE, pattern = "MRM")
Browse code

Use \S4method to document peaks method; see #134

Sebastian Gibb authored on 22/11/2017 21:09:12
Showing 1 changed files
man/peaks.Rd
History View file @ 7189df63a2
... ... 
@@ -45,9 +45,13 @@
45 45
46 46 
  peaksCount(object, scans, ...)
47 47
48 
- peaks(object, ...)
48 
+ \S4method{peaks}{mzRpwiz}(object, scans)
49 
+ \S4method{peaks}{mzRramp}(object, scans)
50 
+ \S4method{peaks}{mzRnetCDF}(object, scans)
49 51
50 
- spectra(object, ...) ## same as peaks
52 
+ \S4method{spectra}{mzRpwiz}(object, scans)   ## same as peaks
53 
+ \S4method{spectra}{mzRramp}(object, scans)
54 
+ \S4method{spectra}{mzRnetCDF}(object, scans)
51 55
52 56 
  get3Dmap(object, scans, lowMz, highMz, resMz, ...)
53 57
... ... 
@@ -66,7 +70,7 @@
66 70 
   \item{object}{An instantiated \code{mzR} object.}
67 71
68 72 
   \item{scans}{A \code{numeric} specifying which scans to
69 
-    return. Optional for the \code{header}, \code{peaks}, \code{scans}
73 
+    return. Optional for the \code{header}, \code{peaks}, \code{spectra}
70 74 
     and \code{peaksCount} methods. If ommited, the requested data for
71 75 
     all peaks is returned. }
72 76
... ... 
@@ -177,7 +181,7 @@
177 181 
  colnames(header(mz))
178 182 
  close(mz)
179 183
180 
- ## A shortgun LCMSMS experiment
184 
+ ## A shotgun LCMSMS experiment
181 185 
  f <- proteomics(full.names = TRUE,
182 186 
                  pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
183 187 
  x <- openMSfile(f, backend = "pwiz")
... ... 
@@ -187,7 +191,10 @@
187 191 
  head(chromatogram(x, 1L)) ## same as tic(x)
188 192 
  str(chromatogram(x)) ## as a list
189 193
190 
- ## An MRM experiment
194 
+ peaks(x) ## extract all peak information
195 
+ peaks(x, scan=4) ## extract just peaks from the 4th scan
196 
+
197 
+ ## An MRM experiment
191 198 
  f <- proteomics(full.names = TRUE, pattern = "MRM")
192 199 
  x <- openMSfile(f, backend = "pwiz")
193 200 
  x
Browse code

Mention that spectrum identifier is variable.

Laurent Gatto authored on 11/09/2017 05:14:35 • GitHub committed on 11/09/2017 05:14:35
Showing 1 changed files
man/peaks.Rd
History View file @ d7e7289bcf
... ... 
@@ -149,7 +149,10 @@
149 149 
   followed by the acquisition number of the spectrum. Also, only the
150 150 
   \code{pwiz} backend supports extraction of the spectras' IDs from
151 151 
   \emph{mzML} files. Thus, only \emph{mzML} files read with
152 
-  \code{backend = "pwiz"} provide the spectrum IDs defined in the file.
152 
+  \code{backend = "pwiz"} provide the spectrum IDs defined in the file.
153 
+  The content of the spectrum identifier depends on the vendor and the
154 
+  instrument acquisition settings and is reported here as a character,
155 
+  in its raw form, without further parsing.
153 156 
 }
154 157
155 158 
 \seealso{
Browse code

Fix typo

Laurent Gatto authored on 10/09/2017 21:15:11 • GitHub committed on 10/09/2017 21:15:11
Showing 1 changed files
man/peaks.Rd
History View file @ b5dd46826a
... ... 
@@ -136,7 +136,7 @@
136 136 
   extracts this number from the spectrum's ID provided in the mzML
137 137 
   file. In contrast, column \code{seqNum} contains the index of each
138 138 
   spectrum within the file and is thus consecutively numbered. Spectra
139 
-  from files with multiple MS levels are linked to each other \emp{via}
139 
+  from files with multiple MS levels are linked to each other \emph{via}
140 140 
   their \code{acquisitionNum}: column \code{precursorScanNum} of an e.g. MS
141 141 
   level 2 spectrum contains the \code{acquisitionNum} of the related MS
142 142 
   level 1 spectrum.
Browse code

Add details for acquisitionNum/precursorScanNum to documentation

jotsetung authored on 10/09/2017 16:58:02
Showing 1 changed files
man/peaks.Rd
History View file @ 7426dfe687
... ... 
@@ -129,6 +129,19 @@
129 129
130 130 
 }
131 131
132 
+\details{
133 
+  The column \code{acquisitionNum} in the \code{data.frame} returned by
134 
+  the \code{header} method contains the index during the scan in which
135 
+  the signal from the spectrum was measured. The \code{pwiz} backend
136 
+  extracts this number from the spectrum's ID provided in the mzML
137 
+  file. In contrast, column \code{seqNum} contains the index of each
138 
+  spectrum within the file and is thus consecutively numbered. Spectra
139 
+  from files with multiple MS levels are linked to each other \emp{via}
140 
+  their \code{acquisitionNum}: column \code{precursorScanNum} of an e.g. MS
141 
+  level 2 spectrum contains the \code{acquisitionNum} of the related MS
142 
+  level 1 spectrum.
143 
+}
144 
+
132 145 
 \note{
133 146 
   Spectrum identifiers are only specified in \emph{mzML} files, thus,
134 147 
   for all other file types the column \code{"spectrumId"} of the result
Browse code

Update documentation

jotsetung authored on 06/09/2017 13:52:46
Showing 1 changed files
man/peaks.Rd
History View file @ 2ddfafdd33
... ... 
@@ -90,14 +90,15 @@
90 90 
   will return a numeric of length \code{n}.
91 91
92 92 
   The \code{\link{header}} function returns a list containing
93 
-  \code{seqNum}, \code{acquisitionNum} , \code{msLevel},
93 
+  \code{seqNum}, \code{acquisitionNum}, \code{msLevel},
94 94 
   \code{peaksCount}, \code{totIonCurrent}, \code{retentionTime} (in
95 95 
   seconds), \code{basePeakMZ}, \code{basePeakIntensity},
96 96 
   \code{collisionEnergy}, \code{ionisationEnergy}, \code{lowM},
97 97 
   \code{highMZ}, \code{precursorScanNum}, \code{precursorMZ},
98 98 
   \code{precursorCharge}, \code{precursorIntensity},
99 99 
   \code{mergedScan}, \code{mergedResultScanNum},
100 
-  \code{mergedResultStartScanNum} and \code{mergedResultEndScanNum},
100 
+  \code{mergedResultStartScanNum}, \code{mergedResultEndScanNum},
101 
+  \code{spectrumId} and
101 102 
   \code{injectionTime} (ion injection time, in seconds) when available
102 103 
   in the original file. If multiple scans are queried, a
103 104 
   \code{data.frame} is returned with the scans reported along the
... ... 
@@ -128,6 +129,16 @@
128 129
129 130 
 }
130 131
132 
+\note{
133 
+  Spectrum identifiers are only specified in \emph{mzML} files, thus,
134 
+  for all other file types the column \code{"spectrumId"} of the result
135 
+  \code{data.frame} returned by \code{header} contains \code{"scan="}
136 
+  followed by the acquisition number of the spectrum. Also, only the
137 
+  \code{pwiz} backend supports extraction of the spectras' IDs from
138 
+  \emph{mzML} files. Thus, only \emph{mzML} files read with
139 
+  \code{backend = "pwiz"} provide the spectrum IDs defined in the file.
140 
+}
141 
+
131 142 
 \seealso{
132 143 
   \code{\link{instrumentInfo}} for metadata access and the
133 144 
   \code{"\linkS4class{mzR}"} class.
Browse code

Merge branch 'master' into write_support

jotsetung authored on 10/07/2017 11:29:35
Showing 0 changed files
Browse code

specify full name as pattern for get the small TMT Erwinia subset

Laurent authored on 23/06/2017 15:24:36
Showing 1 changed files
man/peaks.Rd
History View file @ d05a987e4e
... ... 
@@ -148,7 +148,8 @@
148 148 
  close(mz)
149 149
150 150 
  ## A shortgun LCMSMS experiment
151 
- f <- proteomics(full.names = TRUE, pattern = "^TMT")[2]
151 
+ f <- proteomics(full.names = TRUE,
152 
+                 pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
152 153 
  x <- openMSfile(f, backend = "pwiz")
153 154 
  x
154 155 
  nChrom(x)
Browse code

Enable MS data write support

- export writeMSData and copyWriteMSData functions.
- Add related unit tests and documentation.

jotsetung authored on 23/06/2017 14:15:37
Showing 1 changed files
man/peaks.Rd
History View file @ d4bcbe1386
... ... 
@@ -131,6 +131,9 @@
131 131 
 \seealso{
132 132 
   \code{\link{instrumentInfo}} for metadata access and the
133 133 
   \code{"\linkS4class{mzR}"} class.
134 
+
135 
+  \code{\link{writeMSData}} and \code{\link{copyWriteMSData}} for
136 
+  functions to write MS data in \emph{mzML} or \code{mzXML} format.
134 137 
 }
135 138
136 139 
 \author{
Browse code

make sure use only 1 TMT raw file

Laurent authored on 23/06/2017 04:55:06
Showing 1 changed files
man/peaks.Rd
History View file @ e616a776cb
... ... 
@@ -148,7 +148,7 @@
148 148 
  close(mz)
149 149
150 150 
  ## A shortgun LCMSMS experiment
151 
- f <- proteomics(full.names = TRUE, pattern = "^TMT")
151 
+ f <- proteomics(full.names = TRUE, pattern = "^TMT")[2]
152 152 
  x <- openMSfile(f, backend = "pwiz")
153 153 
  x
154 154 
  nChrom(x)
Browse code

add retention and injection time units

Laurent authored on 13/06/2017 12:01:08
Showing 1 changed files
man/peaks.Rd
History View file @ 81475c01e2
... ... 
@@ -91,16 +91,17 @@
91 91
92 92 
   The \code{\link{header}} function returns a list containing
93 93 
   \code{seqNum}, \code{acquisitionNum} , \code{msLevel},
94 
-  \code{peaksCount}, \code{totIonCurrent}, \code{retentionTime},
95 
-  \code{basePeakMZ}, \code{basePeakIntensity}, \code{collisionEnergy},
96 
-  \code{ionisationEnergy}, \code{lowM}, \code{highMZ},
97 
-  \code{precursorScanNum}, \code{precursorMZ}, \code{precursorCharge},
98 
-  \code{precursorIntensity}, \code{mergedScan},
99 
-  \code{mergedResultScanNum}, \code{mergedResultStartScanNum} and
100 
-  \code{mergedResultEndScanNum}, \code{injectionTime} (ion injection
101 
-  time) when available in the original file. If
102 
-  multiple scans are queried, a \code{data.frame} is returned with the
103 
-  scans reported along the rows.
94 
+  \code{peaksCount}, \code{totIonCurrent}, \code{retentionTime} (in
95 
+  seconds), \code{basePeakMZ}, \code{basePeakIntensity},
96 
+  \code{collisionEnergy}, \code{ionisationEnergy}, \code{lowM},
97 
+  \code{highMZ}, \code{precursorScanNum}, \code{precursorMZ},
98 
+  \code{precursorCharge}, \code{precursorIntensity},
99 
+  \code{mergedScan}, \code{mergedResultScanNum},
100 
+  \code{mergedResultStartScanNum} and \code{mergedResultEndScanNum},
101 
+  \code{injectionTime} (ion injection time, in seconds) when available
102 
+  in the original file. If multiple scans are queried, a
103 
+  \code{data.frame} is returned with the scans reported along the
104 
+  rows.
104 105
105 106 
   The \code{get3Dmap} function performs a simple resampling between
106 107 
   \code{lowMz} and \code{highMz} with \code{reMz} resolution. A matrix
Browse code

Report ion injection time in header of pwiz backend

- Add a column injectionTime to the data.frame returned by the header
function (all backends).
- Pwiz backend extracts the ion injection time.
- Update relevant documentation and add unit test(s).

jotsetung authored on 13/06/2017 09:53:14
Showing 1 changed files
man/peaks.Rd
History View file @ 6523a40958
... ... 
@@ -97,7 +97,8 @@
97 97 
   \code{precursorScanNum}, \code{precursorMZ}, \code{precursorCharge},
98 98 
   \code{precursorIntensity}, \code{mergedScan},
99 99 
   \code{mergedResultScanNum}, \code{mergedResultStartScanNum} and
100 
-  \code{mergedResultEndScanNum}, when available in the original file. If
100 
+  \code{mergedResultEndScanNum}, \code{injectionTime} (ion injection
101 
+  time) when available in the original file. If
101 102 
   multiple scans are queried, a \code{data.frame} is returned with the
102 103 
   scans reported along the rows.
103 104
Browse code

merge conflicts

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@126123 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 24/01/2017 21:20:43
Showing 1 changed files
man/peaks.Rd
History View file @ 96ea799f1c
... ... 
@@ -5,11 +5,42 @@
5 5 
 \alias{peaksCount}
6 6 
 \alias{get3Dmap}
7 7
8 
+\alias{header,mzRramp,missing-method}
9 
+\alias{header,mzRramp,numeric-method}
10 
+\alias{header,mzRpwiz,missing-method}
11 
+\alias{header,mzRpwiz,numeric-method}
12 
+\alias{header,mzRnetCDF,missing-method}
13 
+\alias{header,mzRnetCDF,numeric-method}
14 
+
15 
+\alias{peaksCount,mzRramp,missing-method}
16 
+\alias{peaksCount,mzRramp,numeric-method}
17 
+\alias{peaksCount,mzRpwiz,missing-method}
18 
+\alias{peaksCount,mzRpwiz,numeric-method}
19 
+\alias{peaks,mzRramp-method}
20 
+\alias{spectra,mzRramp-method}
21 
+\alias{peaks,mzRpwiz-method}
22 
+\alias{spectra,mzRpwiz-method}
23 
+\alias{peaks,mzRnetCDF-method}
24 
+\alias{spectra,mzRnetCDF-method}
25 
+
26 
+\alias{get3Dmap,mzRramp-method}
27 
+\alias{get3Dmap,mzRpwiz-method}
28 
+
29 
+\alias{chromatogram,mzRpwiz-method}
30 
+\alias{chromatograms,mzRpwiz-method}
31 
+\alias{tic,mzRpwiz-method}
32 
+\alias{nChrom}
33 
+\alias{chromatogram}
34 
+\alias{chromatograms}
35 
+\alias{tic}
36 
+
37 
+
8 38 
 \title{
9 39 
   Access the raw data from an \code{mzR} object.
10 40 
 }
11 41
12 42 
 \usage{
43 
+
13 44 
  header(object, scans, ...)
14 45
15 46 
  peaksCount(object, scans, ...)
... ... 
@@ -19,30 +50,44 @@
19 50 
  spectra(object, ...) ## same as peaks
20 51
21 52 
  get3Dmap(object, scans, lowMz, highMz, resMz, ...)
53 
+
54 
+ chromatogram(object, ...)
55 
+
56 
+ chromatograms(object, ...) ## same as chromatogram
57 
+
58 
+ tic(object, ...)
59 
+
60 
+ nChrom(object)
61 
+
22 62 
 }
23 63
24 64 
 \arguments{
65 
+
25 66 
   \item{object}{An instantiated \code{mzR} object.}
67 
+
26 68 
   \item{scans}{A \code{numeric} specifying which scans to
27 
-    return. Optional for the \code{header}, \code{peaks}, \code{scans} and
28 
-    \code{peaksCount} methods. If ommited, the requested data for all
29 
-    peaks is returned. }
30 
-  \item{lowMz, highMz}{\code{Numeric}s defining the m/z range to be returned.}
69 
+    return. Optional for the \code{header}, \code{peaks}, \code{scans}
70 
+    and \code{peaksCount} methods. If ommited, the requested data for
71 
+    all peaks is returned. }
72 
+
73 
+  \item{lowMz, highMz}{\code{Numeric}s defining the m/z range to be
74 
+    returned.}
75 
+
31 76 
   \item{resMz}{a \code{numeric} defining the m/z resolution.}
77 
+
32 78 
   \item{...}{Other arguments. A \code{scan} parameter can be passed to
33 
-    \code{peaks}.}
34 
-}
79 
+    \code{peaks}.}  }
35 80
36 81 
 \description{
37 82
38 83 
   Access the MS raw data. The \code{peaks}, \code{spectra} (can be used
39 84 
   interchangeably) and \code{peaksCount} functions return the (m/z,
40 85 
   intensity) pairs and the number peaks in the
41 
-  spectrum/spectra. \code{peaks} and \code{spectra} return a single matrix
42 
-  if \code{scans} is a \code{numeric} of length 1 and a list of matrices
43 
-  if several scans are asked for or no \code{scans} argument is provided
44 
-  (i.e all spectra in the oject are retured). \code{peaksCount} will
45 
-  return a numeric of length \code{n}.
86 
+  spectrum/spectra. \code{peaks} and \code{spectra} return a single
87 
+  matrix if \code{scans} is a \code{numeric} of length 1 and a list of
88 
+  matrices if several scans are asked for or no \code{scans} argument is
89 
+  provided (i.e all spectra in the oject are retured). \code{peaksCount}
90 
+  will return a numeric of length \code{n}.
46 91
47 92 
   The \code{\link{header}} function returns a list containing
48 93 
   \code{seqNum}, \code{acquisitionNum} , \code{msLevel},
... ... 
@@ -56,10 +101,29 @@
56 101 
   multiple scans are queried, a \code{data.frame} is returned with the
57 102 
   scans reported along the rows.
58 103
59 
- The \code{get3Dmap} function performs a simple resampling between
60 
- \code{lowMz} and \code{highMz} with \code{reMz} resolution. A matrix of
61 
- dimensions \code{length(scans)} times \code{seq(lowMz,highMz,resMz)} is
62 
- returned.
104 
+  The \code{get3Dmap} function performs a simple resampling between
105 
+  \code{lowMz} and \code{highMz} with \code{reMz} resolution. A matrix
106 
+  of dimensions \code{length(scans)} times
107 
+  \code{seq(lowMz,highMz,resMz)} is returned.
108 
+
109 
+  The \code{chromatogram} (\code{chromatograms}) accessors return
110 
+  chromatograms for the MS file handle. If a single index is provided,
111 
+  as \code{data.frame} containing the retention time (1st columns) and
112 
+  intensities (2nd column) is returned. The name of the former is always
113 
+  \code{time}, while the latter will depend on the run parameters.
114 
+
115 
+  If more than 1 or no chromatogram indices are provided, then a list of
116 
+  chromatograms is returned; either those passed as argument or all of
117 
+  them. By default, the first (and possibly only) chromatogram is the
118 
+  total ion count, which can also be accessed with the \code{tic}
119 
+  method.
120 
+
121 
+  The \code{nChrom} function returns the number of chromatograms,
122 
+  including the total ion chromatogram.
123 
+
124 
+  Note that access to chromatograms is only supported in the \code{pwiz}
125 
+  backend.
126 
+
63 127 
 }
64 128
65 129 
 \seealso{
... ... 
@@ -80,4 +144,22 @@
80 144 
  runInfo(mz)
81 145 
  colnames(header(mz))
82 146 
  close(mz)
147 
+
148 
+ ## A shortgun LCMSMS experiment
149 
+ f <- proteomics(full.names = TRUE, pattern = "^TMT")
150 
+ x <- openMSfile(f, backend = "pwiz")
151 
+ x
152 
+ nChrom(x)
153 
+ head(tic(x))
154 
+ head(chromatogram(x, 1L)) ## same as tic(x)
155 
+ str(chromatogram(x)) ## as a list
156 
+
157 
+ ## An MRM experiment
158 
+ f <- proteomics(full.names = TRUE, pattern = "MRM")
159 
+ x <- openMSfile(f, backend = "pwiz")
160 
+ x
161 
+ nChrom(x)
162 
+ head(tic(x))
163 
+ head(chromatogram(x, 1L)) ## same as tic(x)
164 
+ str(chromatogram(x, 10:12))
83 165 
 }
Browse code

fix merge conflict

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@125207 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 15/12/2016 11:00:07
Showing 1 changed files
man/peaks.Rd
History View file @ 1b4b2b9059
... ... 
@@ -1,5 +1,6 @@
1 1 
 \name{peaks}
2 2 
 \alias{peaks}
3 
+\alias{spectra}
3 4 
 \alias{header}
4 5 
 \alias{peaksCount}
5 6 
 \alias{get3Dmap}
... ... 
@@ -13,7 +14,9 @@
13 14
14 15 
  peaksCount(object, scans, ...)
15 16
16 
- peaks(object, ...)
17 
+ peaks(object, ...)
18 
+
19 
+ spectra(object, ...) ## same as peaks
17 20
18 21 
  get3Dmap(object, scans, lowMz, highMz, resMz, ...)
19 22 
 }
... ... 
@@ -21,7 +24,7 @@
21 24 
 \arguments{
22 25 
   \item{object}{An instantiated \code{mzR} object.}
23 26 
   \item{scans}{A \code{numeric} specifying which scans to
24 
-    return. Optional for the \code{header}, \code{peaks} and
27 
+    return. Optional for the \code{header}, \code{peaks}, \code{scans} and
25 28 
     \code{peaksCount} methods. If ommited, the requested data for all
26 29 
     peaks is returned. }
27 30 
   \item{lowMz, highMz}{\code{Numeric}s defining the m/z range to be returned.}
... ... 
@@ -31,25 +34,27 @@
31 34 
 }
32 35
33 36 
 \description{
34 
-  Access the MS raw data. The \code{peaks} and \code{peaksCount}
35 
-  functions return the (m/z,intensity) pairs and the number peaks in the
36 
-  spectrum/spectra. \code{peaks} returns a single matrix if \code{scans}
37 
-  is a \code{numeric} of length 1 and a list of matrices if several scans are
38 
-  asked for or no \code{scans} argument is provided (i.e all spectra in
39 
-  the oject are retured). \code{peaksCount} will return a numeric of
40 
-  length \code{n}.
37 
+
38 
+  Access the MS raw data. The \code{peaks}, \code{spectra} (can be used
39 
+  interchangeably) and \code{peaksCount} functions return the (m/z,
40 
+  intensity) pairs and the number peaks in the
41 
+  spectrum/spectra. \code{peaks} and \code{spectra} return a single matrix
42 
+  if \code{scans} is a \code{numeric} of length 1 and a list of matrices
43 
+  if several scans are asked for or no \code{scans} argument is provided
44 
+  (i.e all spectra in the oject are retured). \code{peaksCount} will
45 
+  return a numeric of length \code{n}.
41 46
42 47 
   The \code{\link{header}} function returns a list containing
43 
- \code{seqNum}, \code{acquisitionNum} , \code{msLevel},
44 
- \code{peaksCount}, \code{totIonCurrent}, \code{retentionTime},
45 
- \code{basePeakMZ}, \code{basePeakIntensity}, \code{collisionEnergy},
46 
- \code{ionisationEnergy}, \code{lowM}, \code{highMZ},
47 
- \code{precursorScanNum}, \code{precursorMZ}, \code{precursorCharge},
48 
- \code{precursorIntensity}, \code{mergedScan},
49 
- \code{mergedResultScanNum}, \code{mergedResultStartScanNum} and
50 
- \code{mergedResultEndScanNum}, when available in the original file. If
51 
- multiple scans are queried, a \code{data.frame} is returned with the
52 
- scans reported along the rows.
48 
+  \code{seqNum}, \code{acquisitionNum} , \code{msLevel},
49 
+  \code{peaksCount}, \code{totIonCurrent}, \code{retentionTime},
50 
+  \code{basePeakMZ}, \code{basePeakIntensity}, \code{collisionEnergy},
51 
+  \code{ionisationEnergy}, \code{lowM}, \code{highMZ},
52 
+  \code{precursorScanNum}, \code{precursorMZ}, \code{precursorCharge},
53 
+  \code{precursorIntensity}, \code{mergedScan},
54 
+  \code{mergedResultScanNum}, \code{mergedResultStartScanNum} and
55 
+  \code{mergedResultEndScanNum}, when available in the original file. If
56 
+  multiple scans are queried, a \code{data.frame} is returned with the
57 
+  scans reported along the rows.
53 58
54 59 
  The \code{get3Dmap} function performs a simple resampling between
55 60 
  \code{lowMz} and \code{highMz} with \code{reMz} resolution. A matrix of
... ... 
@@ -66,7 +71,6 @@
66 71 
   Steffen Neumann and Laurent Gatto
67 72 
 }
68 73
69 
-
70 74 
 \examples{
71 75 
  library(msdata)
72 76 
  filepath <- system.file("microtofq", package = "msdata")
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6599b4e00f742fc668f41353450efbaf98f0bbf1

using the generic functions from ProtGenerics and BiocGenerics



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@100003 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 28/02/2015 14:26:11
Showing 1 changed files
man/peaks.Rd
History View file @ 3820996d60
... ... 
@@ -13,7 +13,7 @@
13 13
14 14 
  peaksCount(object, scans, ...)
15 15
16 
- peaks(object, scans, ...)
16 
+ peaks(object, ...)
17 17
18 18 
  get3Dmap(object, scans, lowMz, highMz, resMz, ...)
19 19 
 }
... ... 
@@ -26,7 +26,8 @@
26 26 
     peaks is returned. }
27 27 
   \item{lowMz, highMz}{\code{Numeric}s defining the m/z range to be returned.}
28 28 
   \item{resMz}{a \code{numeric} defining the m/z resolution.}
29 
-  \item{...}{Other arguments. Currently ignored.}
29 
+  \item{...}{Other arguments. A \code{scan} parameter can be passed to
30 
+    \code{peaks}.}
30 31 
 }
31 32
32 33 
 \description{
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 130 commits.

Commit information:

Commit id: 289dc240065888efcaa22ae75951e81f94fc800f

Fix package description after merge

Committed by: Steffen Neumann
Author Name: Steffen Neumann
Commit date: 2014-09-28 17:21:35 +0200
Author date: 2014-09-28 17:21:35 +0200

Commit id: 88248e8d6d86bb54dc260f0c55608dd1a949ade4

merged gsoc into master

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-27 08:49:45 +0100
Author date: 2014-09-27 08:49:45 +0100

Commit id: bb01e0fe0b4f04335925472a7c2b91bd22b57755

included KK's segfault patch and fixed unit test accordingly

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-27 08:44:50 +0100
Author date: 2014-09-27 08:44:50 +0100

Commit id: 708bd0b8ac4b2b5bae9a9b91588a260f2eeefb46

add message about pwiz backend in Bioc 3.1

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-25 01:20:52 +0100
Author date: 2014-09-25 01:20:52 +0100

Commit id: 4c1410ec3c8f153ad0a4b04722cad5a7d77cfd4c

restoring ramp as default backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-25 01:06:21 +0100
Author date: 2014-09-25 01:06:21 +0100

Commit id: c5d60529934813456555934bbeed29502100b41b

show pwiz method

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 21:09:38 +0100
Author date: 2014-09-21 21:09:38 +0100

Commit id: 20bfbfa1db25ec247f2313804d9b73c086a2d920

add close,mzRpwiz-method alias

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 21:04:48 +0100
Author date: 2014-09-21 21:04:48 +0100

Commit id: f80ecdc2a7f14c311b42ad279c62307a6e0aad30

test that close(pwiz) works

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 20:45:50 +0100
Author date: 2014-09-21 20:45:50 +0100

Commit id: d18dc8b0c7197c72b1bb2a70e7becfe983ced9a1

fixed signature for pwiz close method

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 20:44:41 +0100
Author date: 2014-09-21 20:44:41 +0100

Commit id: c0d7451e6b31068cde89f08ac5037a1509857cc5

fix codoc mismatch

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 19:02:00 +0100
Author date: 2014-09-21 19:02:00 +0100

Commit id: 14974a3d0890a7e2a1a7179aaa483e20a5700ef9

add close for pwiz backend to news

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:58:06 +0100
Author date: 2014-09-21 18:58:06 +0100

Commit id: c9d2bbb339c0ecdc9870dbd7a59bfbb94ef67f73

dummy close for pwiz backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:56:48 +0100
Author date: 2014-09-21 18:56:48 +0100

Commit id: 6d608b453328d6c751dc828d2586b016eb17b095

more close calls to remove for pwiz backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:52:55 +0100
Author date: 2014-09-21 18:52:55 +0100

Commit id: 5650801e07df64e2d74302ec98a31938bb62f11f

no isInitialised with pwiz

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 18:41:57 +0100
Author date: 2014-09-21 18:41:57 +0100

Commit id: 2a3d0eeb24673eb74c3ffa38fefb1883f9bee15d

no close with pwiz

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:46:38 +0100
Author date: 2014-09-21 17:46:38 +0100

Commit id: b3ae014569b6e46ccb6b396dfb9320dd7ba8fb16

bump version to avoid confusions

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:30:28 +0100
Author date: 2014-09-21 17:30:28 +0100

Commit id: a1bd596ffbeef73b4b505342f45742f9997e33d1

using pwiz as default raw data backend

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-21 17:29:02 +0100
Author date: 2014-09-21 17:29:02 +0100

Commit id: 51b4ea21d9cf034d54b0911bf281af3a937375de

Steffen's changes in v 1.11.11

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 16:21:14 +0100
Author date: 2014-09-20 16:21:14 +0100

Commit id: 81cde1ca48974585c9d6f51927087a922b13dd89

add new length to doc header

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 16:06:46 +0100
Author date: 2014-09-20 16:06:46 +0100

Commit id: 3fe883cb7ecad4867908fb907374a4df63b50a1f

show and length mzRident methods

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-09-20 15:56:26 +0100
Author date: 2014-09-20 15:56:26 +0100

Commit id: 3efb44e00fb94cdf0eb8207634218cbb47ab1b54

VignetteBuilder: knitr

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-27 01:03:36 +0100
Author date: 2014-08-27 01:03:36 +0100

Commit id: 73b0f902dfaa53f359318708f0606dc1f4677057

BiocStyle vig

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-26 23:59:29 +0100
Author date: 2014-08-26 23:59:29 +0100

Commit id: 185f281d07ed7b4a7f093eaf7b61271a88c85e20

update readme

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-26 23:20:02 +0100
Author date: 2014-08-26 23:20:02 +0100

Commit id: d5cc992e128594d331592b2bd57871fabf6737c9

update to build

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:41:17 +0100
Author date: 2014-08-17 22:41:17 +0100

Commit id: 27318416c94859102a061838a1a3f83d378414e3

bump to 1.99

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:12:44 +0100
Author date: 2014-08-17 22:12:44 +0100

Commit id: 13caefb4d4b469f0406ed96509ea4cebce8235b0

pulled from https://github.com/thirdwing/mzR

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-08-17 22:00:57 +0100
Author date: 2014-08-17 22:00:57 +0100

Commit id: 14822efb6c2238eda371718043bec9cc8fb27558

doc

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-16 22:06:51 -0400
Author date: 2014-08-16 22:06:51 -0400

Commit id: 323424443efac769c436fb87128fad64a0358187

R_init_mzR.c

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-10 00:46:14 -0400
Author date: 2014-08-10 00:46:14 -0400

Commit id: a91c0601e674efbb6949331a53ea9c6af53a4ba5

vignettes

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-06 21:03:23 -0400
Author date: 2014-08-06 21:03:23 -0400

Commit id: 4607e0a595f60a083d1eb90b804348ac5a8c1fb4

update with msdata

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-05 12:33:40 -0400
Author date: 2014-08-05 12:33:40 -0400

Commit id: cc09a790eda22b7d64226116ada89bad9089e0b2

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-04 22:29:15 -0400
Author date: 2014-08-04 22:29:15 -0400

Commit id: fac511ee0f7841791bbf5380f2c948fd045b3adb

unit test against mzID

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-04 22:16:03 -0400
Author date: 2014-08-04 22:16:03 -0400

Commit id: 449952e31fe354b2589d8a723a4f8a842812ede6

enzymes() returns data.frame

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:29:59 -0400
Author date: 2014-08-03 16:29:59 -0400

Commit id: 874fba33e8029023d5e3bbd168dc998d51544c9d

writing support dropped

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:14:26 -0400
Author date: 2014-08-03 16:14:26 -0400

Commit id: 338f3e80dd8f98419555ab1a4aa443e14d089f24

modifications()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 16:02:20 -0400
Author date: 2014-08-03 16:02:20 -0400

Commit id: 34ee62ee27e7b012b9ce2bd696d63e5f80185200

psms() update

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 15:41:36 -0400
Author date: 2014-08-03 15:41:36 -0400

Commit id: b8bdea9a1e2a7ab3410eea5c26566ef74e488d95

score()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-03 14:14:53 -0400
Author date: 2014-08-03 14:14:53 -0400

Commit id: a42f1195b3f0b40c28aa2acfb782e517633206c9

psms()

Committed by: qkou
Author Name: qkou
Commit date: 2014-08-03 13:54:34 -0400
Author date: 2014-08-03 13:54:34 -0400

Commit id: 6c2a87019e3b328dbecc1a965d3e41e6539e0d90

para() update, numeric correction

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-08-02 23:57:41 -0400
Author date: 2014-08-02 23:57:41 -0400

Commit id: 119edf40600beb8e3b8e8006a0d955a887d06b1d

update para()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-30 10:54:40 -0400
Author date: 2014-07-30 10:54:40 -0400

Commit id: 69ac718d0418f2ab3ba824a735975ae6c04aec00

update database()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-30 10:38:42 -0400
Author date: 2014-07-30 10:38:42 -0400

Commit id: f7818556b2e1e3296a727eca6d2853a8b7a16b12

clean

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 21:35:59 -0400
Author date: 2014-07-29 21:35:59 -0400

Commit id: f67403a92b6beca4128c36b42367414463234253

database()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 21:33:07 -0400
Author date: 2014-07-29 21:33:07 -0400

Commit id: 8b0255a9c7da6ccc6c7796f49f608b792bac0dfe

para()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-29 20:33:14 -0400
Author date: 2014-07-29 20:33:14 -0400

Commit id: 183afed91ad6beb07fffb5cbe4673773619d938b

Rd

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-29 00:36:40 -0400
Author date: 2014-07-29 00:36:40 -0400

Commit id: 73d380115e205eedc211869d6eace3564b3fc1cf

modified: vignettes/mzR.Rnw

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-27 00:49:10 -0400
Author date: 2014-07-27 00:49:10 -0400

Commit id: 93214634ff41a9da84019320dfe6314cb7f94422

score

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-26 19:42:34 -0400
Author date: 2014-07-26 19:42:34 -0400

Commit id: cbdee47033cf10927b0dc33a02208c9ff9d89771

same header info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-22 12:45:46 -0400
Author date: 2014-07-22 12:45:46 -0400

Commit id: 1e6ebe39851ecddedf01daa2c69fcd1f2dba906c

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: inst/unitTests/runit.backends.R modified: man/metadata.Rd modified: man/mzR-class.Rd

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-18 00:40:10 -0400
Author date: 2014-07-18 00:40:10 -0400

Commit id: 0ed92085be5af56a78cdf0f1732a356c48d7a0f9

1.11.10

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-17 21:31:27 -0400
Author date: 2014-07-17 21:31:27 -0400

Commit id: b6e254b2cca93778bfcdc549b75052d0b19bb2bb

fixed

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-16 01:40:10 -0400
Author date: 2014-07-16 01:40:10 -0400

Commit id: 096aa2a6f5aebb5b99bc2e22a0fb023b1353b141

Merge pull request #3 from lgatto/master

fix backend checking
Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-07-15 21:20:15 -0400
Author date: 2014-07-15 21:20:15 -0400

Commit id: 6d8623c47c0b53e6805b9757c178c4639319a29d

fix backend checking

Committed by: Laurent
Author Name: Laurent
Commit date: 2014-07-15 23:32:46 +0100
Author date: 2014-07-15 23:32:46 +0100

Commit id: 9060e3435a76ace952d915c3bb993e04ac93f12a

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-14 10:52:41 -0400
Author date: 2014-07-14 10:52:41 -0400

Commit id: 068ec46671400a2db3bfb10f001f30599b8495e8

modified: ChangeLog

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 17:29:16 -0400
Author date: 2014-07-12 17:29:16 -0400

Commit id: a8f42c9de00ed64470733eb5c63567e99d40e867

more info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 14:57:33 -0400
Author date: 2014-07-12 14:57:33 -0400

Commit id: 4a88ad7c2c8ec911c44a45d16dedced9530505c2

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 14:13:29 -0400
Author date: 2014-07-12 14:13:29 -0400

Commit id: 935d44c5a52b895fe6ff663c062e006e4f25fab0

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 13:52:33 -0400
Author date: 2014-07-12 13:52:33 -0400

Commit id: f1c05ff287215f385938a116042d09bcea2aae88

modified: R/methods-mzRident.R modified: man/mzR-class.Rd modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-12 11:20:58 -0400
Author date: 2014-07-12 11:20:58 -0400

Commit id: ca620536203355349c7267ad15a2ab6a2d248319

pass R CMD check

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-12 00:36:08 -0400
Author date: 2014-07-12 00:36:08 -0400

Commit id: add1d1c98fe60955953036641671527337e89363

modified: R/methods-mzRident.R modified: man/metadata.Rd modified: man/mzR-class.Rd modified: src/Makevars modified: src/Makevars.win

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 23:48:02 -0400
Author date: 2014-07-11 23:48:02 -0400

Commit id: 050051489df378a26aa97cccfefbf7ebe4102ef5

pepInfo()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 18:10:10 -0400
Author date: 2014-07-11 18:10:10 -0400

Commit id: f093e39599ea2357c91816b7ff9de102f33e8e68

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 15:12:28 -0400
Author date: 2014-07-11 15:12:28 -0400

Commit id: 3dc85db859c4d36040d3edb9ceb57074b0476f2d

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 14:49:47 -0400
Author date: 2014-07-11 14:49:47 -0400

Commit id: ab1261cb3bfe1c02de5f7a053e6de5223686488d

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-11 13:47:12 -0400
Author date: 2014-07-11 13:47:12 -0400

Commit id: 01a4a2be981724624719580cd8e4f0866091f295

version

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 01:48:50 -0400
Author date: 2014-07-11 01:48:50 -0400

Commit id: 5f49d13b736cebd65484a5993cdcce253853d4e7

remove mz5

Committed by: qkou
Author Name: qkou
Commit date: 2014-07-11 01:41:00 -0400
Author date: 2014-07-11 01:41:00 -0400

Commit id: fb3dbe2f1bf007cd033fd803426d4be2e362b3e2

Update H5public.h

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-07-07 08:46:19 -0400
Author date: 2014-07-07 08:46:19 -0400

Commit id: 2446f08fdadd11c38a1cb54dddfe1e52b1a7bca9

modified: src/pwiz/utility/chemistry/Chemistry.hpp modified: src/pwiz/utility/misc/Std.hpp modified: src/pwiz/utility/misc/sha1calc.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 19:41:41 -0400
Author date: 2014-07-04 19:41:41 -0400

Commit id: b7c28c0db06b2dc9f8f5a7dcd218b7581ffd8121

compiled

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 18:05:54 -0400
Author date: 2014-07-04 18:05:54 -0400

Commit id: 1ffe5c024dafd51c2342f4d1dd930cb8d67d8041

modified: DESCRIPTION modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-04 10:09:46 -0400
Author date: 2014-07-04 10:09:46 -0400

Commit id: 06e03716f187508072c33d3f0e9e79e135b22c05

modified: src/Makevars modified: src/hdf5/src/H5public.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 22:32:09 -0400
Author date: 2014-07-03 22:32:09 -0400

Commit id: 488ed2bd55151ece46c8cb5ac1df11f73b7c47a3

modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 21:48:39 -0400
Author date: 2014-07-03 21:48:39 -0400

Commit id: 06f4d0a3832e47ad4a69e53d7b9b751dbb9f2770

modified: src/hdf5/src/H5public.h modified: src/pwiz/utility/misc/SHA1.cpp modified: src/pwiz/utility/misc/SHA1.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-07-03 21:47:50 -0400
Author date: 2014-07-03 21:47:50 -0400

Commit id: ff58989379a67f20ac8797ba437d430d8b5a2d62

modified: src/RcppIdent.cpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-30 09:42:05 -0400
Author date: 2014-06-30 09:42:05 -0400

Commit id: 58dfa68675768c13950299c43229c1b0f1f1824b

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 21:17:18 -0400
Author date: 2014-06-28 21:17:18 -0400

Commit id: 6c228ae30c477e76add7e3ea805e386f1a0d862d

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 20:16:55 -0400
Author date: 2014-06-28 20:16:55 -0400

Commit id: 464d4e83a9e06732f7c3f1a0172a9cb2bbd53943

modified: src/RcppIdent.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 17:21:01 -0400
Author date: 2014-06-28 17:21:01 -0400

Commit id: ed36541a5fc99192f9df55222f2a2d9a6352ae33

idInfo

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 17:02:20 -0400
Author date: 2014-06-28 17:02:20 -0400

Commit id: 1ed6dceee93d2f57a66a94b15774212403d42200

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRident.R modified: src/RcppIdent.cpp modified: src/RcppIdent.h modified: src/RcppIdentModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 15:19:47 -0400
Author date: 2014-06-28 15:19:47 -0400

Commit id: 47b2a99876650729a329ebeebc174d9873919667

modified: DESCRIPTION

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 13:12:13 -0400
Author date: 2014-06-28 13:12:13 -0400

Commit id: ecad541c1e2d92f7be63433c5bf362d7b7f955b2

mzid supported done

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-28 13:04:27 -0400
Author date: 2014-06-28 13:04:27 -0400

Commit id: 684340ce7ee5b8fadbd4dfa839e3b0d7ba9b1c91

mzid file support

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-28 01:02:19 -0400
Author date: 2014-06-28 01:02:19 -0400

Commit id: 7382b1321539a2838ae75da6f9c1ff9cbe98bb6b

mzid

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 23:38:36 -0400
Author date: 2014-06-27 23:38:36 -0400

Commit id: 5423b4c653762d90ce6d4bf7dcf1d591a2a9987f

modified: R/methods-mzRpwiz.R modified: R/zzz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 23:27:36 -0400
Author date: 2014-06-27 23:27:36 -0400

Commit id: 9e20328e920207328eb68b9fa59c198d0d634a0f

Update AllGenerics.R

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-27 22:52:37 -0400
Author date: 2014-06-27 22:52:37 -0400

Commit id: 19731b9e51b72027eb02ee6be5aa7343c5b12ace

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRpwiz.R modified: man/metadata.Rd modified: man/mzR-class.Rd modified: man/openMSfile.Rd modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h modified: src/RcppPwizModule.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 22:03:31 -0400
Author date: 2014-06-27 22:03:31 -0400

Commit id: 94ac2b4ba810d0f820a9266be782667e375ede9a

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-27 10:15:58 -0400
Author date: 2014-06-27 10:15:58 -0400

Commit id: 1259a8db48d4f7aa9ffe403dd5ee574bbfd238fb

modified: R/zzz.R modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-27 00:44:31 -0400
Author date: 2014-06-27 00:44:31 -0400

Commit id: 9791bc574989cdefe279071dbf3a47232e1d8c86

identadata src

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-27 00:22:35 -0400
Author date: 2014-06-27 00:22:35 -0400

Commit id: ede49e01e23c6586777d72fdd0dfef4bd40729f2

software info

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 22:20:57 -0400
Author date: 2014-06-26 22:20:57 -0400

Commit id: 431b2b42a93ff52a05d82801d1830ba81c72f18f

writeMSfile()

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 21:53:11 -0400
Author date: 2014-06-26 21:53:11 -0400

Commit id: 53a7a31378bd42adcf779cd1fbe9e2d052a507d7

deleted: src/hdf5/c++/src/H5 deleted: src/hdf5/c++/src/H5DataTy deleted: src/pwiz/data/common/BinaryIndexSt deleted: src/pwiz/data/common/ParamT deleted: src/pwiz/data/m deleted: src/pwiz/data/msdata/BinaryDataEnc deleted: src/pwiz/data/msdata/Chroma deleted: src/pwiz/data/msdata/MSNu deleted: src/pwiz/data/msdata/Seri deleted: src/pwiz/data/msdata/Serializer deleted: src/pwiz/data/msdata/Serializer_mz deleted: src/pwiz/data/msdata/Sp deleted: src/pwiz/data/msdata/Spec deleted: src/pwiz/data/msdata/mz5/Refer deleted: src/pwiz/utility/mis deleted: src/pwiz/utility/misc/IntegerS

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 19:04:22 -0400
Author date: 2014-06-26 19:04:22 -0400

Commit id: 359a40045162a49d94d68f0d60f2c6bb43970a2c

modified: NAMESPACE modified: R/AllGenerics.R modified: R/io.R modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h modified: src/RcppPwizModule.cpp new file: src/boost/filesystem/src/operations new file: src/hdf5/c++/src/H5 new file: src/hdf5/c++/src/H5DataTy new file: src/pwiz/data/common/BinaryIndexSt new file: src/pwiz/data/common/ParamT new file: src/pwiz/data/m new file: src/pwiz/data/msdata/BinaryDataEnc new file: src/pwiz/data/msdata/Chroma new file: src/pwiz/data/msdata/MSNu new file: src/pwiz/data/msdata/Seri new file: src/pwiz/data/msdata/Serializer new file: src/pwiz/data/msdata/Serializer_mz new file: src/pwiz/data/msdata/Sp new file: src/pwiz/data/msdata/Spec new file: src/pwiz/data/msdata/mz5/Refer new file: src/pwiz/utility/mis new file: src/pwiz/utility/misc/IntegerS

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 19:00:48 -0400
Author date: 2014-06-26 19:00:48 -0400

Commit id: 2ce04488e7a8e623a7dfd2b9408da0b9dd5059a4

modified: inst/unitTests/runit.backends.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 15:59:21 -0400
Author date: 2014-06-26 15:59:21 -0400

Commit id: 3103fd4fa92ddd63700c8b5940344db44e97be09

modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 13:33:44 -0400
Author date: 2014-06-26 13:33:44 -0400

Commit id: 329f7c1201360f5ebf5703d4837b25ae332e7a85

modified: man/metadata.Rd modified: man/mzR-class.Rd modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 11:35:13 -0400
Author date: 2014-06-26 11:35:13 -0400

Commit id: 0adf852da9ccec69103038ca96b30e8715d3c898

modified: inst/unitTests/runit.backends.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-26 11:20:03 -0400
Author date: 2014-06-26 11:20:03 -0400

Commit id: 219b5287ca5531577b4a6c80f403957ddef5ab94

modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-26 01:33:43 -0400
Author date: 2014-06-26 01:33:43 -0400

Commit id: 14316dcb1c16ca922d9962ed9ecdaac324e1a151

deleted: src/R_init_mzR.c modified: src/RcppPwiz.cpp deleted: src/ramp_base64.cpp deleted: src/ramp_base64.h

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-26 01:04:14 -0400
Author date: 2014-06-26 01:04:14 -0400

Commit id: efb21501a1b05b680b3d35aa124216f9977b5993

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 23:44:07 -0400
Author date: 2014-06-25 23:44:07 -0400

Commit id: 4e9e1dec2879178547d681603aec46259a6a9978

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:54:26 -0400
Author date: 2014-06-25 22:54:26 -0400

Commit id: 0e7fc23b1ff7508fed6331c0e517a8dc6fa33a0c

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:28:24 -0400
Author date: 2014-06-25 22:28:24 -0400

Commit id: 9ad55a2cdd89791bf75ad23f0ee91b3fc70624ad

mz5

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-25 22:13:35 -0400
Author date: 2014-06-25 22:13:35 -0400

Commit id: c9fecd83ebf31f142c22030f4593fe5ac675323a

modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 23:31:33 -0400
Author date: 2014-06-24 23:31:33 -0400

Commit id: 4edf517724950d6771fd19c979a460711baa5891

modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 23:01:49 -0400
Author date: 2014-06-24 23:01:49 -0400

Commit id: 22ca998b6b6d3a7496f293f44909436a5b7d8ad0

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-24 21:31:58 -0400
Author date: 2014-06-24 21:31:58 -0400

Commit id: 6beb4ce5c49cafa644766e23453ed6d10bb89c34

modified: man/metadata.Rd modified: man/mzR-class.Rd

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-22 12:02:07 -0400
Author date: 2014-06-22 12:02:07 -0400

Commit id: dc5e65d93bb67d1b4a1488b90099946e22eed13c

deleted: .travis.yml

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-22 11:26:02 -0400
Author date: 2014-06-22 11:26:02 -0400

Commit id: be53359804d6c7416c715c3eb259fb931c6c117a

modified: .travis.yml modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:33:37 -0400
Author date: 2014-06-21 21:33:37 -0400

Commit id: 1afd9887dac232f3e72fe9d20d44a72b42e28461

deleted: .Rinstignore

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:27:46 -0400
Author date: 2014-06-21 21:27:46 -0400

Commit id: bd4c954bd246787137eb0d961a91bb80b774cb6a

new file: .Rbuildignore new file: .travis.yml

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:25:47 -0400
Author date: 2014-06-21 21:25:47 -0400

Commit id: 3bc8fcca8002a62458a2b2dd1c6b7cf6a8cfab9f

fixed error on windows and snow leopard

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-21 21:18:50 -0400
Author date: 2014-06-21 21:18:50 -0400

Commit id: ed9c622443eb992cf3322d687312e3f56bf8be72

Update Makevars.win

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-15 00:55:16 +0800
Author date: 2014-06-15 00:55:16 +0800

Commit id: bf8c7bd931cd93b5db6d84c9c1bf323ea7702e74

new file: src/boost/signals/connection.hpp new file: src/boost/signals/detail/config.hpp new file: src/boost/signals/detail/gen_signal_N.pl new file: src/boost/signals/detail/named_slot_map.hpp new file: src/boost/signals/detail/signal_base.hpp new file: src/boost/signals/detail/signals_common.hpp new file: src/boost/signals/detail/slot_call_iterator.hpp new file: src/boost/signals/signal0.hpp new file: src/boost/signals/signal1.hpp new file: src/boost/signals/signal10.hpp new file: src/boost/signals/signal2.hpp new file: src/boost/signals/signal3.hpp new file: src/boost/signals/signal4.hpp new file: src/boost/signals/signal5.hpp new file: src/boost/signals/signal6.hpp new file: src/boost/signals/signal7.hpp new file: src/boost/signals/signal8.hpp new file: src/boost/signals/signal9.hpp new file: src/boost/signals/signal_template.hpp new file: src/boost/signals/slot.hpp new file: src/boost/signals/trackable.hpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-14 12:52:52 -0400
Author date: 2014-06-14 12:52:52 -0400

Commit id: 5ac3655c7e81f429859eb6b509208f8ec785e1f9

modified: src/Makevars.win

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-07 11:42:14 -0400
Author date: 2014-06-07 11:42:14 -0400

Commit id: f9f42e3d83adbaf98a201e50866821bc0e43598a

modified: ChangeLog modified: src/RcppPwiz.cpp modified: src/hdf5/src/H5FDmulti.c

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-07 11:24:01 -0400
Author date: 2014-06-07 11:24:01 -0400

Commit id: d8d6f92e46efa93f8234e542b1c4f8f98cee59e5

modified: R/zzz.R.in

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 17:28:36 -0400
Author date: 2014-06-06 17:28:36 -0400

Commit id: e64a8bb7bb7988047466848e5b449038ae9460b3

modified: R/zzz.R modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 16:40:29 -0400
Author date: 2014-06-06 16:40:29 -0400

Commit id: 0a44cc02ea9b5417ac51f60632fc1b6100c6d160

modified: src/Makevars

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 16:01:08 -0400
Author date: 2014-06-06 16:01:08 -0400

Commit id: 4d19d457031e0ae9af343a44774f5deebae01cc8

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-06 14:16:37 -0400
Author date: 2014-06-06 14:16:37 -0400

Commit id: effcb581a573e13b7b7cc9b459ef2dec4885b4be

modified: src/RcppPwiz.cpp

Committed by: kouqiang
Author Name: kouqiang
Commit date: 2014-06-06 04:33:43 -0400
Author date: 2014-06-06 04:33:43 -0400

Commit id: 028f6748d4cf81d47569edcd67fe25064b084e60

modified: NAMESPACE modified: R/AllGenerics.R modified: R/methods-mzRpwiz.R modified: src/RcppPwiz.cpp

Committed by: thirdwing
Author Name: thirdwing
Commit date: 2014-06-04 23:21:43 -0400
Author date: 2014-06-04 23:21:43 -0400

Commit id: d95b557d2c637630ca784889cd0ef1f56b8423d5

Update methods-mzRpwiz.R

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:51:47 -0400
Author date: 2014-06-04 21:51:47 -0400

Commit id: aad52653c2ceb33655364d5a39c0559225746cfb

Update RcppPwizModule.cpp

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:50:32 -0400
Author date: 2014-06-04 21:50:32 -0400

Commit id: 4fda90cc08feb731aeb65c6015a033fbe46c372e

Update RcppPwiz.cpp

Committed by: Qiang Kou
Author Name: Qiang Kou
Commit date: 2014-06-04 21:48:06 -0400
Author date: 2014-06-04 21:48:06 -0400

Commit id: 660d2e984fabdd20997ff8b648d361c7d9aae711

modified: src/RcppPwiz.cpp modified: src/RcppPwiz.h

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-02 13:07:57 -0400
Author date: 2014-06-02 13:07:57 -0400

Commit id: ec6bbdf496a57f2f39b2e4c3bbada75a060e5bbe

modified: src/boost_aux/boost/utility/singleton.hpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-06-02 09:21:07 -0400
Author date: 2014-06-02 09:21:07 -0400

Commit id: a093954cb779467026288c7f51cca083e0a20661

modified: src/pwiz/data/msdata/ramp/ramp.cpp

Committed by: qkou
Author Name: qkou
Commit date: 2014-05-29 07:36:21 -0400
Author date: 2014-05-29 07:36:21 -0400

Commit id: 4510a1cda50ee8f1f43b667297918dcffed45af2

modified: src/Makevars modified: src/cramp.h modified: src/pwiz/data/msdata/ramp/ramp.cpp deleted: src/ramp.cpp deleted: src/ramp.h modified: src/rampR.cpp deleted: src/ramp_base64.cpp deleted: src/ramp_base64.h

Committed by: qkou
Author Name: qkou
Commit date: 2014-05-28 20:17:42 -0400
Author date: 2014-05-28 20:17:42 -0400


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@94635 bc3139a8-67e5-0310-9ffc-ced21a209358

s.neumann authored on 28/09/2014 18:06:01
Showing 1 changed files
man/peaks.Rd
History View file @ 84a4b1664f
... ... 
@@ -70,9 +70,9 @@
70 70 
  library(msdata)
71 71 
  filepath <- system.file("microtofq", package = "msdata")
72 72 
  file <- list.files(filepath, pattern="MM14.mzML",
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-                    full.names=TRUE, recursive = TRUE)
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-  mz <- openMSfile(file)
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-  runInfo(mz)
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-  colnames(header(mz))
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-  close(mz)
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+                     full.names=TRUE, recursive = TRUE)
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+ mz <- openMSfile(file)
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+ runInfo(mz)
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+ colnames(header(mz))
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+ close(mz)
78 78 
 }
Browse code

Added the mzR package to the repository.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@57456 bc3139a8-67e5-0310-9ffc-ced21a209358

c.wong authored on 15/08/2011 19:53:29
Showing 1 changed files
man/peaks.Rd
History View file @ bcff5d52a8
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,78 @@
1 
+\name{peaks}
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+\alias{peaks}
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+\alias{header}
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+\alias{peaksCount}
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+\alias{get3Dmap}
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+
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+\title{
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+  Access the raw data from an \code{mzR} object.
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+}
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+
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+\usage{
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+ header(object, scans, ...)
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+
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+ peaksCount(object, scans, ...)
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+
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+ peaks(object, scans, ...)
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+
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+ get3Dmap(object, scans, lowMz, highMz, resMz, ...)
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+}
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+
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+\arguments{
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+  \item{object}{An instantiated \code{mzR} object.}
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+  \item{scans}{A \code{numeric} specifying which scans to
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+    return. Optional for the \code{header}, \code{peaks} and
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+    \code{peaksCount} methods. If ommited, the requested data for all
26 
+    peaks is returned. }
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+  \item{lowMz, highMz}{\code{Numeric}s defining the m/z range to be returned.}
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+  \item{resMz}{a \code{numeric} defining the m/z resolution.}
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+  \item{...}{Other arguments. Currently ignored.}
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+}
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+
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+\description{
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+  Access the MS raw data. The \code{peaks} and \code{peaksCount}
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+  functions return the (m/z,intensity) pairs and the number peaks in the
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+  spectrum/spectra. \code{peaks} returns a single matrix if \code{scans}
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+  is a \code{numeric} of length 1 and a list of matrices if several scans are
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+  asked for or no \code{scans} argument is provided (i.e all spectra in
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+  the oject are retured). \code{peaksCount} will return a numeric of
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+  length \code{n}.
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+
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+  The \code{\link{header}} function returns a list containing
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+ \code{seqNum}, \code{acquisitionNum} , \code{msLevel},
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+ \code{peaksCount}, \code{totIonCurrent}, \code{retentionTime},
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+ \code{basePeakMZ}, \code{basePeakIntensity}, \code{collisionEnergy},
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+ \code{ionisationEnergy}, \code{lowM}, \code{highMZ},
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+ \code{precursorScanNum}, \code{precursorMZ}, \code{precursorCharge},
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+ \code{precursorIntensity}, \code{mergedScan},
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+ \code{mergedResultScanNum}, \code{mergedResultStartScanNum} and
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+ \code{mergedResultEndScanNum}, when available in the original file. If
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+ multiple scans are queried, a \code{data.frame} is returned with the
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+ scans reported along the rows.
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+
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+ The \code{get3Dmap} function performs a simple resampling between
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+ \code{lowMz} and \code{highMz} with \code{reMz} resolution. A matrix of
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+ dimensions \code{length(scans)} times \code{seq(lowMz,highMz,resMz)} is
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+ returned.
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+}
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+
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+\seealso{
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+  \code{\link{instrumentInfo}} for metadata access and the
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+  \code{"\linkS4class{mzR}"} class.
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+}
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+
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+\author{
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+  Steffen Neumann and Laurent Gatto
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+}
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+
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+
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+\examples{
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+ library(msdata)
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+ filepath <- system.file("microtofq", package = "msdata")
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+ file <- list.files(filepath, pattern="MM14.mzML",
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+                    full.names=TRUE, recursive = TRUE)
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+  mz <- openMSfile(file)
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+  runInfo(mz)
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+  colnames(header(mz))
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+  close(mz)
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+}