Browse code

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

Laurent authored on 23/06/2017 15:24:36
Showing 5 changed files

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@@ -14,7 +14,8 @@ test_chromatograms1 <- function() {
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 }
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 test_chromatograms2 <- function() {
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-    f <- proteomics(full.names = TRUE, pattern = "^TMT")
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+    f <- proteomics(full.names = TRUE,
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+                    pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
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     x <- openMSfile(f, backend = "pwiz")
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     checkIdentical(nChrom(x), 1L)   
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     checkIdentical(tic(x), chromatogram(x, 1L))
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@@ -1,6 +1,7 @@
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 test_isolationWindow <- function() {
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     library("msdata")
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-    f <- msdata::proteomics(full.names = TRUE, pattern = "TMT_")
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+    f <- msdata::proteomics(full.names = TRUE,
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+                            pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
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     rw1 <- openMSfile(f, backend = "Ramp")
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     rw2 <- openMSfile(f, backend = "pwiz")
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     i1 <- isolationWindow(f)
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@@ -118,7 +118,8 @@ test_getScanHeaderInfo <- function() {
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     close(ramp)
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     ## Again for an MSn mzml file.
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-    file <- msdata::proteomics(full.names = TRUE, pattern = "TMT_Erwinia")
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+    file <- msdata::proteomics(full.names = TRUE,
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+                               pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
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     mzml <- openMSfile(file, backend = "pwiz")
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     ramp <- openMSfile(file, backend = "Ramp")
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     ## Read single scan header.
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@@ -51,7 +51,8 @@
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 \examples{
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 library("msdata")
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-f <- msdata::proteomics(full.names = TRUE, pattern = "TMT_")[2]
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+f <- msdata::proteomics(full.names = TRUE,
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+                        pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
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 isolationWindow(f)
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 rw <- openMSfile(f)
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@@ -148,7 +148,8 @@
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  close(mz)
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  ## A shortgun LCMSMS experiment 
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- f <- proteomics(full.names = TRUE, pattern = "^TMT")[2]
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+ f <- proteomics(full.names = TRUE,
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+                 pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
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  x <- openMSfile(f, backend = "pwiz")
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  x
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  nChrom(x)