1. CNEr
  2. NAMESPACE
Browse code

version 1.13.1

fix the DBI import

Ge Tan authored on 03/07/2017 12:48:07
Showing 1 changed files
NAMESPACE
History View file @ 1b64794
... ... 
@@ -19,7 +19,8 @@ importMethodsFrom(GenomeInfoDb, seqnames, seqlengths, seqinfo, as.data.frame,
19 19 
 importMethodsFrom(GenomicRanges, reduce, "strand<-", strand, start, end,
20 20 
                                  findOverlaps, coverage, grglist)
21 21 
 importMethodsFrom(XVector, subseq)
22 
-importMethodsFrom(RSQLite, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)
22 
+importMethodsFrom(DBI, dbGetQuery)
23 
+importMethodsFrom(RSQLite, dbConnect, dbDisconnect, dbWriteTable)
23 24 
 importMethodsFrom(methods, initialize, show)
24 25 
 importMethodsFrom(Biostrings, compareStrings)
25 26 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
Browse code

donot export addAncestorGO now

Ge Tan authored on 22/04/2017 12:40:25
Showing 1 changed files
NAMESPACE
History View file @ a3a9c44
... ... 
@@ -156,7 +156,7 @@ export(
156 156 
   plotCNEWidth, plotCNEDistribution,
157 157
158 158 
   # GO.R
159 
-  addAncestorGO,
159 
+  ## addAncestorGO,
160 160
161 161 
   ## AssemblyStats.R
162 162 
   N50, N90
Browse code

version 1.11.8

Add function to find ancestor GO IDs

Ge Tan authored on 12/04/2017 20:21:45
Showing 1 changed files
NAMESPACE
History View file @ ff9fd4f
... ... 
@@ -155,6 +155,9 @@ export(
155 155 
   # CNE-utils.R
156 156 
   plotCNEWidth, plotCNEDistribution,
157 157
158 
+  # GO.R
159 
+  addAncestorGO,
160 
+
158 161 
   ## AssemblyStats.R
159 162 
   N50, N90
160 163 
 )
Browse code

version 1.11.7

Update from Bioconductor and remove `fill` in `geom_text`

Ge Tan authored on 23/02/2017 12:07:45
Showing 1 changed files
NAMESPACE
History View file @ 61ec06c
... ... 
@@ -5,7 +5,7 @@ import(BiocGenerics)
5 5 
 ### Import S4 classes defined in other packages
6 6 
 ###
7 7 
 importClassesFrom(methods, ANY, character, integer, missing)
8 
-importClassesFrom(S4Vectors, List, characterORNULL, DataFrame, Pairs)
8 
+importClassesFrom(S4Vectors, List, character_OR_NULL, DataFrame, Pairs)
9 9 
 importClassesFrom(GenomicRanges, GRanges)
10 10 
 importClassesFrom(Biostrings, DNAStringSet)
11 11
... ... 
@@ -89,7 +89,6 @@ exportMethods(
89 89 
   syntenicDotplot,
90 90
91 91 
   ## Axt-methods.R
92 
-  #  mismatchSummary
93 92 
   summary
94 93 
 )
95 94
... ... 
@@ -104,7 +103,6 @@ export(
104 103 
   binRangesFromCoordRange,
105 104 
   binRestrictionString,
106 105 
   readCNERangesFromSQLite,
107 
-  #queryAnnotationSQLite,
108 106 
   fetchChromSizes,
109 107
110 108 
   ## Axt-class.R
... ... 
@@ -118,6 +116,7 @@ export(
118 116
119 117 
   ## CNE-class.R
120 118 
   CNE,
119 
+
121 120 
   ## GRangePairs-class.R
122 121 
   GRangePairs,
123 122
... ... 
@@ -131,14 +130,7 @@ export(
131 130 
   read.rmskFasta,
132 131
133 132 
   ## ceScan.R
134 
-
135 133 
   blatCNE,
136 
-  #ceScanOneStep,
137 
-
138 
-  ## makeGeneDbFromUCSC.r
139 
-  #supportedUCSCtables,
140 
-  #queryrefGene, queryknownGene, queryensGene,
141 
-  #makeGeneDbFromUCSC,
142 134
143 135 
   ## WholeGenomeAlignment.R
144 136 
   lastz,
Browse code

version 1.11.5

Add the function of makeAxtTracks

Ge Tan authored on 01/12/2016 21:31:42
Showing 1 changed files
NAMESPACE
History View file @ 5550270
... ... 
@@ -111,7 +111,7 @@ export(
111 111 
   Axt,
112 112
113 113 
   ## Axt-methods.R
114 
-  #dotplotAxt,
114 
+  makeAxtTracks,
115 115
116 116 
   ## subAxt-methods.R
117 117 
   psubAxt,
Browse code

version 1.11.3

Add the function of mapping KEGG IDs and Gene IDs

Ge Tan authored on 25/10/2016 15:12:06
Showing 1 changed files
NAMESPACE
History View file @ c092f67
... ... 
@@ -62,6 +62,7 @@ importFrom(GO.db, GOCCANCESTOR, GOCCOFFSPRING, GOCCCHILDREN,
62 62 
                   GOMFANCESTOR, GOMFOFFSPRING, GOMFCHILDREN)
63 63 
 importFrom("grDevices", "jpeg", "pdf", "png", "postscript")
64 64 
 importFrom(R.utils, gunzip, gzip)
65 
+importFrom(KEGGREST, keggGet)
65 66
66 67 
 ### -----------------------------------------------------------------
67 68 
 ### Export S4 classes defined in CNEr
Browse code

version 1.9.40

Add read.rmskFasta function

Ge Tan authored on 20/09/2016 10:30:22
Showing 1 changed files
NAMESPACE
History View file @ 0288d5e
... ... 
@@ -35,7 +35,8 @@ importMethodsFrom(GenomicAlignments, last)
35 35 
 importFrom(GenomeInfoDb, Seqinfo)
36 36 
 importFrom(GenomicRanges, GRanges)
37 37 
 importFrom(GenomicAlignments, explodeCigarOps, CIGAR_OPS, explodeCigarOpLengths)
38 
-importFrom(Biostrings, DNAStringSet, DNA_BASES, fasta.seqlengths)
38 
+importFrom(Biostrings, DNAStringSet, DNA_BASES, fasta.seqlengths,
39 
+           readBStringSet)
39 40 
 importFrom(RSQLite, SQLite)
40 41 
 importFrom(methods, is, new, "as", "extends", "validObject")
41 42 
 importFrom(rtracklayer, TwoBitFile)
... ... 
@@ -126,6 +127,7 @@ export(
126 127 
   writeAxt,
127 128 
   read.rmMask.GRanges,
128 129 
   saveCNEToSQLite,
130 
+  read.rmskFasta,
129 131
130 132 
   ## ceScan.R
131 133
Browse code

use read.delim instead of read_tsv

Ge Tan authored on 31/08/2016 11:46:49
Showing 1 changed files
NAMESPACE
History View file @ 9295830
... ... 
@@ -46,7 +46,7 @@ importFrom(S4Vectors, .Call2, queryHits, subjectHits, DataFrame,
46 46 
            isTRUEorFALSE, isSingleString, queryLength, subjectLength)
47 47 
 importFrom(tools, file_ext)
48 48 
 importFrom(parallel, mcmapply)
49 
-importFrom(utils, download.file, read.table, write.table)
49 
+importFrom(utils, download.file, read.table, write.table, read.delim)
50 50 
 importFrom("stats", "setNames")
51 51 
 importFrom(reshape2, melt)
52 52 
 importFrom(ggplot2, ggplot, aes, aes_q, aes_string, geom_tile, theme_bw,
Browse code

version 1.9.37

remove the power law test. Problem of importing "dist_rand"

Ge Tan authored on 22/08/2016 16:51:33
Showing 1 changed files
NAMESPACE
History View file @ b3a8f2f
... ... 
@@ -53,7 +53,7 @@ importFrom(ggplot2, ggplot, aes, aes_q, aes_string, geom_tile, theme_bw,
53 53 
     xlab, ylab, ggtitle, geom_point, scale_colour_manual,
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     scale_fill_continuous, geom_text, scale_x_continuous, scale_y_continuous,
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     geom_segment, facet_wrap)
56 
-importFrom(poweRlaw, bootstrap_p, estimate_pars, estimate_xmin)
56 
+importFrom(poweRlaw, estimate_pars, estimate_xmin)
57 57 
 importFrom("graphics", "lines", "par", "plot", "text")
58 58 
 importFrom(annotate, getGOTerm)
59 59 
 importFrom(GO.db, GOCCANCESTOR, GOCCOFFSPRING, GOCCCHILDREN,
Browse code

version 1.9.36

remove function queryCNEData

Ge Tan authored on 22/08/2016 14:50:02
Showing 1 changed files
NAMESPACE
History View file @ 97a64ac
... ... 
@@ -137,9 +137,6 @@ export(
137 137 
   #queryrefGene, queryknownGene, queryensGene,
138 138 
   #makeGeneDbFromUCSC,
139 139
140 
-  ## DB.R
141 
-  queryCNEData,
142 
-
143 140 
   ## WholeGenomeAlignment.R
144 141 
   lastz,
145 142 
   lavToPsl,
Browse code

version 1.9.35

readAxt for gzip files works on Windows platform now

Ge Tan authored on 15/08/2016 14:29:38
Showing 1 changed files
NAMESPACE
History View file @ 0c9a962
... ... 
@@ -60,6 +60,7 @@ importFrom(GO.db, GOCCANCESTOR, GOCCOFFSPRING, GOCCCHILDREN,
60 60 
                   GOBPANCESTOR, GOBPOFFSPRING, GOBPCHILDREN,
61 61 
                   GOMFANCESTOR, GOMFOFFSPRING, GOMFCHILDREN)
62 62 
 importFrom("grDevices", "jpeg", "pdf", "png", "postscript")
63 
+importFrom(R.utils, gunzip, gzip)
63 64
64 65 
 ### -----------------------------------------------------------------
65 66 
 ### Export S4 classes defined in CNEr
Browse code

version 1.9.33

function to make Ancora files

Ge Tan authored on 12/08/2016 19:26:30
Showing 1 changed files
NAMESPACE
History View file @ b617c9e
... ... 
@@ -154,7 +154,7 @@ export(
154 154 
   makeGRBs,
155 155
156 156 
   ## Ancora.R
157 
-  readAncora, readAncoraIntoSQLite, makeCNEDensity,
157 
+  readAncora, readAncoraIntoSQLite, makeCNEDensity, makeAncoraFiles,
158 158
159 159 
   ## plot.R
160 160 
   CNEDensity,
Browse code

seqinfo when readAncora

Ge Tan authored on 08/08/2016 14:55:12
Showing 1 changed files
NAMESPACE
History View file @ 5d131a6
... ... 
@@ -59,6 +59,8 @@ importFrom(annotate, getGOTerm)
59 59 
 importFrom(GO.db, GOCCANCESTOR, GOCCOFFSPRING, GOCCCHILDREN,
60 60 
                   GOBPANCESTOR, GOBPOFFSPRING, GOBPCHILDREN,
61 61 
                   GOMFANCESTOR, GOMFOFFSPRING, GOMFCHILDREN)
62 
+importFrom("grDevices", "jpeg", "pdf", "png", "postscript")
63 
+
62 64 
 ### -----------------------------------------------------------------
63 65 
 ### Export S4 classes defined in CNEr
64 66 
 ###
Browse code

version 1.9.31

Add code for potential GO analysis

Ge Tan authored on 05/08/2016 18:01:49
Showing 1 changed files
NAMESPACE
History View file @ b1d3dc2
... ... 
@@ -55,7 +55,10 @@ importFrom(ggplot2, ggplot, aes, aes_q, aes_string, geom_tile, theme_bw,
55 55 
     geom_segment, facet_wrap)
56 56 
 importFrom(poweRlaw, bootstrap_p, estimate_pars, estimate_xmin)
57 57 
 importFrom("graphics", "lines", "par", "plot", "text")
58 
-
58 
+importFrom(annotate, getGOTerm)
59 
+importFrom(GO.db, GOCCANCESTOR, GOCCOFFSPRING, GOCCCHILDREN,
60 
+                  GOBPANCESTOR, GOBPOFFSPRING, GOBPCHILDREN,
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+                  GOMFANCESTOR, GOMFOFFSPRING, GOMFCHILDREN)
59 62 
 ### -----------------------------------------------------------------
60 63 
 ### Export S4 classes defined in CNEr
61 64 
 ###
Browse code

version 1.9.30

bigwig files are also exported.

Ge Tan authored on 04/08/2016 14:26:58
Showing 1 changed files
NAMESPACE
History View file @ b773c56
... ... 
@@ -12,7 +12,8 @@ importClassesFrom(Biostrings, DNAStringSet)
12 12 
 ### -----------------------------------------------------------------
13 13 
 ### Import S4 methods defined in other packages
14 14 
 ###
15 
-importMethodsFrom(rtracklayer, import.bed, export.bedGraph, export.bed)
15 
+importMethodsFrom(rtracklayer, import.bed, export.bedGraph, export.bed,
16 
+                  export.bw)
16 17 
 importMethodsFrom(GenomeInfoDb, seqnames, seqlengths, seqinfo, as.data.frame,
17 18 
                   genome, "genome<-", "seqlengths<-")
18 19 
 importMethodsFrom(GenomicRanges, reduce, "strand<-", strand, start, end,
Browse code

version 1.9.29

bedGraph instead of bigwig

Ge Tan authored on 26/07/2016 18:07:16
Showing 1 changed files
NAMESPACE
History View file @ c65d5e3
... ... 
@@ -12,7 +12,7 @@ importClassesFrom(Biostrings, DNAStringSet)
12 12 
 ### -----------------------------------------------------------------
13 13 
 ### Import S4 methods defined in other packages
14 14 
 ###
15 
-importMethodsFrom(rtracklayer, import.bed, export.bw, export.bed)
15 
+importMethodsFrom(rtracklayer, import.bed, export.bedGraph, export.bed)
16 16 
 importMethodsFrom(GenomeInfoDb, seqnames, seqlengths, seqinfo, as.data.frame,
17 17 
                   genome, "genome<-", "seqlengths<-")
18 18 
 importMethodsFrom(GenomicRanges, reduce, "strand<-", strand, start, end,
... ... 
@@ -148,7 +148,7 @@ export(
148 148 
   makeGRBs,
149 149
150 150 
   ## Ancora.R
151 
-  readAncora, readAncoraIntoSQLite, makeBedBigWig,
151 
+  readAncora, readAncoraIntoSQLite, makeCNEDensity,
152 152
153 153 
   ## plot.R
154 154 
   CNEDensity,
Browse code

version 1.9.28

Function to export bed and bigwig for CNEs

Ge Tan authored on 25/07/2016 10:00:39
Showing 1 changed files
NAMESPACE
History View file @ 774a714
... ... 
@@ -12,7 +12,7 @@ importClassesFrom(Biostrings, DNAStringSet)
12 12 
 ### -----------------------------------------------------------------
13 13 
 ### Import S4 methods defined in other packages
14 14 
 ###
15 
-importMethodsFrom(rtracklayer, import.bed)
15 
+importMethodsFrom(rtracklayer, import.bed, export.bw, export.bed)
16 16 
 importMethodsFrom(GenomeInfoDb, seqnames, seqlengths, seqinfo, as.data.frame,
17 17 
                   genome, "genome<-", "seqlengths<-")
18 18 
 importMethodsFrom(GenomicRanges, reduce, "strand<-", strand, start, end,
... ... 
@@ -148,7 +148,7 @@ export(
148 148 
   makeGRBs,
149 149
150 150 
   ## Ancora.R
151 
-  readAncora, readAncoraIntoSQLite,
151 
+  readAncora, readAncoraIntoSQLite, makeBedBigWig,
152 152
153 153 
   ## plot.R
154 154 
   CNEDensity,
Browse code

version 1.9.27

Add plotCNEDistribution

Ge Tan authored on 22/07/2016 09:32:06
Showing 1 changed files
NAMESPACE
History View file @ cc9f90b
... ... 
@@ -23,7 +23,8 @@ importMethodsFrom(methods, initialize, show)
23 23 
 importMethodsFrom(Biostrings, compareStrings)
24 24 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
25 25 
                   showAsCell, extractROWS, mcols, "mcols<-", split, runValue,
26 
-                  as.factor, "%in%", second, "first<-", "second<-")
26 
+                  as.factor, "%in%", second, "first<-", "second<-",
27 
+                  runLength)
27 28 
 importMethodsFrom(IRanges, slice, ranges, "ranges<-")
28 29 
 importMethodsFrom(GenomicAlignments, last)
29 30
... ... 
@@ -50,7 +51,7 @@ importFrom(reshape2, melt)
50 51 
 importFrom(ggplot2, ggplot, aes, aes_q, aes_string, geom_tile, theme_bw,
51 52 
     xlab, ylab, ggtitle, geom_point, scale_colour_manual,
52 53 
     scale_fill_continuous, geom_text, scale_x_continuous, scale_y_continuous,
53 
-    geom_segment)
54 
+    geom_segment, facet_wrap)
54 55 
 importFrom(poweRlaw, bootstrap_p, estimate_pars, estimate_xmin)
55 56 
 importFrom("graphics", "lines", "par", "plot", "text")
56 57
... ... 
@@ -153,7 +154,7 @@ export(
153 154 
   CNEDensity,
154 155
155 156 
   # CNE-utils.R
156 
-  plotCNEWidth,
157 
+  plotCNEWidth, plotCNEDistribution,
157 158
158 159 
   ## AssemblyStats.R
159 160 
   N50, N90
Browse code

version 1.9.25

add new function psubAxt

Ge Tan authored on 20/07/2016 07:26:39
Showing 1 changed files
NAMESPACE
History View file @ 8bcf04c
... ... 
@@ -103,6 +103,9 @@ export(
103 103 
   ## Axt-methods.R
104 104 
   #dotplotAxt,
105 105
106 
+  ## subAxt-methods.R
107 
+  psubAxt,
108 
+
106 109 
   ## CNE-class.R
107 110 
   CNE,
108 111 
   ## GRangePairs-class.R
Browse code

version 1.9.23

simply the code of syntenicDotplot

Ge Tan authored on 19/07/2016 07:28:53
Showing 1 changed files
NAMESPACE
History View file @ 6e41ed0
... ... 
@@ -14,7 +14,7 @@ importClassesFrom(Biostrings, DNAStringSet)
14 14 
 ###
15 15 
 importMethodsFrom(rtracklayer, import.bed)
16 16 
 importMethodsFrom(GenomeInfoDb, seqnames, seqlengths, seqinfo, as.data.frame,
17 
-                  genome, "genome<-")
17 
+                  genome, "genome<-", "seqlengths<-")
18 18 
 importMethodsFrom(GenomicRanges, reduce, "strand<-", strand, start, end,
19 19 
                                  findOverlaps, coverage, grglist)
20 20 
 importMethodsFrom(XVector, subseq)
Browse code

version 1.9.22

Add fixCoordinates function

Ge Tan authored on 15/07/2016 14:42:11
Showing 1 changed files
NAMESPACE
History View file @ c9f8fed
... ... 
@@ -24,7 +24,7 @@ importMethodsFrom(Biostrings, compareStrings)
24 24 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
25 25 
                   showAsCell, extractROWS, mcols, "mcols<-", split, runValue,
26 26 
                   as.factor, "%in%", second, "first<-", "second<-")
27 
-importMethodsFrom(IRanges, slice, ranges)
27 
+importMethodsFrom(IRanges, slice, ranges, "ranges<-")
28 28 
 importMethodsFrom(GenomicAlignments, last)
29 29
30 30 
 ### -----------------------------------------------------------------
... ... 
@@ -168,7 +168,7 @@ exportMethods(
168 168 
   subAxt,
169 169
170 170 
   ## Axt-methods.R
171 
-  matchDistribution,
171 
+  matchDistribution, fixCoordinates,
172 172
173 173 
   # CNE-class.R
174 174 
   CNE12, CNE21,
Browse code

version 1.9.21

GRangePairs is built on Piars

Ge Tan authored on 15/07/2016 13:16:50
Showing 1 changed files
NAMESPACE
History View file @ 1931d17
... ... 
@@ -5,7 +5,7 @@ import(BiocGenerics)
5 5 
 ### Import S4 classes defined in other packages
6 6 
 ###
7 7 
 importClassesFrom(methods, ANY, character, integer, missing)
8 
-importClassesFrom(S4Vectors, List, characterORNULL, DataFrame)
8 
+importClassesFrom(S4Vectors, List, characterORNULL, DataFrame, Pairs)
9 9 
 importClassesFrom(GenomicRanges, GRanges)
10 10 
 importClassesFrom(Biostrings, DNAStringSet)
11 11
... ... 
@@ -23,7 +23,7 @@ importMethodsFrom(methods, initialize, show)
23 23 
 importMethodsFrom(Biostrings, compareStrings)
24 24 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
25 25 
                   showAsCell, extractROWS, mcols, "mcols<-", split, runValue,
26 
-                  as.factor, "%in%")
26 
+                  as.factor, "%in%", second, "first<-", "second<-")
27 27 
 importMethodsFrom(IRanges, slice, ranges)
28 28 
 importMethodsFrom(GenomicAlignments, last)
29 29
... ... 
@@ -41,7 +41,7 @@ importFrom(readr, read_tsv)
41 41 
 importFrom(IRanges, IRanges, IntegerList, RleViewsList)
42 42 
 importFrom(S4Vectors, .Call2, queryHits, subjectHits, DataFrame,
43 43 
            normalizeSingleBracketSubscript, normalizeDoubleBracketSubscript,
44 
-           isTRUEorFALSE, isSingleString)
44 
+           isTRUEorFALSE, isSingleString, queryLength, subjectLength)
45 45 
 importFrom(tools, file_ext)
46 46 
 importFrom(parallel, mcmapply)
47 47 
 importFrom(utils, download.file, read.table, write.table)
... ... 
@@ -65,16 +65,15 @@ exportClasses(Axt,
65 65 
 ### Export S4 methods for generics not defined in CNEr
66 66 
 ###
67 67 
 exportMethods(
68 
-  "[",
69 
-  c,
68 
+#"[",
69 
+ c,
70 70
71 71 
   ## AllClasses.r
72 
-  length,
73 72 
   score,
74 
-  names, seqnames, "names<-", strand,
73 
+  seqnames, strand,
75 74
76 75 
   ## GRangePairs-class.R
77 
-  first, last, grglist, seqinfo, unique,
76 
+  first, last, second, grglist, seqinfo, unique,
78 77
79 78 
   ## GRangePairs-methods.R
80 79 
   syntenicDotplot,
Browse code

version 1.9.18

flexible seqinfo for ceScan

Ge Tan authored on 14/07/2016 13:08:29
Showing 1 changed files
NAMESPACE
History View file @ ff65683
... ... 
@@ -23,7 +23,7 @@ importMethodsFrom(methods, initialize, show)
23 23 
 importMethodsFrom(Biostrings, compareStrings)
24 24 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
25 25 
                   showAsCell, extractROWS, mcols, "mcols<-", split, runValue,
26 
-                  as.factor)
26 
+                  as.factor, "%in%")
27 27 
 importMethodsFrom(IRanges, slice, ranges)
28 28 
 importMethodsFrom(GenomicAlignments, last)
29 29
Browse code

version 1.9.17

add seqinfo into Axt when available.

Ge Tan authored on 14/07/2016 09:27:17
Showing 1 changed files
NAMESPACE
History View file @ 81df7b2
... ... 
@@ -13,7 +13,8 @@ importClassesFrom(Biostrings, DNAStringSet)
13 13 
 ### Import S4 methods defined in other packages
14 14 
 ###
15 15 
 importMethodsFrom(rtracklayer, import.bed)
16 
-importMethodsFrom(GenomeInfoDb, seqnames, seqlengths, seqinfo, as.data.frame)
16 
+importMethodsFrom(GenomeInfoDb, seqnames, seqlengths, seqinfo, as.data.frame,
17 
+                  genome, "genome<-")
17 18 
 importMethodsFrom(GenomicRanges, reduce, "strand<-", strand, start, end,
18 19 
                                  findOverlaps, coverage, grglist)
19 20 
 importMethodsFrom(XVector, subseq)
Browse code

version 1.9.14

syntenicDotplot for GRangePairs

Ge Tan authored on 12/07/2016 15:17:37
Showing 1 changed files
NAMESPACE
History View file @ a3e4b51
... ... 
@@ -48,7 +48,8 @@ importFrom("stats", "setNames")
48 48 
 importFrom(reshape2, melt)
49 49 
 importFrom(ggplot2, ggplot, aes, aes_q, aes_string, geom_tile, theme_bw,
50 50 
     xlab, ylab, ggtitle, geom_point, scale_colour_manual,
51 
-    scale_fill_continuous, geom_text, scale_x_continuous, scale_y_continuous)
51 
+    scale_fill_continuous, geom_text, scale_x_continuous, scale_y_continuous,
52 
+    geom_segment)
52 53 
 importFrom(poweRlaw, bootstrap_p, estimate_pars, estimate_xmin)
53 54 
 importFrom("graphics", "lines", "par", "plot", "text")
54 55
... ... 
@@ -73,6 +74,9 @@ exportMethods(
73 74
74 75 
   ## GRangePairs-class.R
75 76 
   first, last, grglist, seqinfo, unique,
77 
+
78 
+  ## GRangePairs-methods.R
79 
+  syntenicDotplot,
76 80
77 81 
   ## Axt-methods.R
78 82 
   #  mismatchSummary
... ... 
@@ -97,7 +101,7 @@ export(
97 101 
   Axt,
98 102
99 103 
   ## Axt-methods.R
100 
-  dotplotAxt,
104 
+  #dotplotAxt,
101 105
102 106 
   ## CNE-class.R
103 107 
   CNE,
Browse code

Add syntenic dotplot

Ge Tan authored on 24/06/2016 13:57:03
Showing 1 changed files
NAMESPACE
History View file @ ab9e2d2
... ... 
@@ -21,7 +21,8 @@ importMethodsFrom(RSQLite, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)
21 21 
 importMethodsFrom(methods, initialize, show)
22 22 
 importMethodsFrom(Biostrings, compareStrings)
23 23 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
24 
-                  showAsCell, extractROWS, mcols, "mcols<-", split, runValue)
24 
+                  showAsCell, extractROWS, mcols, "mcols<-", split, runValue,
25 
+                  as.factor)
25 26 
 importMethodsFrom(IRanges, slice, ranges)
26 27 
 importMethodsFrom(GenomicAlignments, last)
27 28
... ... 
@@ -33,7 +34,7 @@ importFrom(GenomicRanges, GRanges)
33 34 
 importFrom(GenomicAlignments, explodeCigarOps, CIGAR_OPS, explodeCigarOpLengths)
34 35 
 importFrom(Biostrings, DNAStringSet, DNA_BASES, fasta.seqlengths)
35 36 
 importFrom(RSQLite, SQLite)
36 
-importFrom(methods, is, new)
37 
+importFrom(methods, is, new, "as", "extends", "validObject")
37 38 
 importFrom(rtracklayer, TwoBitFile)
38 39 
 importFrom(readr, read_tsv)
39 40 
 importFrom(IRanges, IRanges, IntegerList, RleViewsList)
... ... 
@@ -46,8 +47,8 @@ importFrom(utils, download.file, read.table, write.table)
46 47 
 importFrom("stats", "setNames")
47 48 
 importFrom(reshape2, melt)
48 49 
 importFrom(ggplot2, ggplot, aes, aes_q, aes_string, geom_tile, theme_bw,
49 
-    xlab, ylab, ggtitle,
50 
-    scale_fill_continuous, geom_text)
50 
+    xlab, ylab, ggtitle, geom_point, scale_colour_manual,
51 
+    scale_fill_continuous, geom_text, scale_x_continuous, scale_y_continuous)
51 52 
 importFrom(poweRlaw, bootstrap_p, estimate_pars, estimate_xmin)
52 53 
 importFrom("graphics", "lines", "par", "plot", "text")
53 54
... ... 
@@ -94,6 +95,10 @@ export(
94 95
95 96 
   ## Axt-class.R
96 97 
   Axt,
98 
+
99 
+  ## Axt-methods.R
100 
+  dotplotAxt,
101 
+
97 102 
   ## CNE-class.R
98 103 
   CNE,
99 104 
   ## GRangePairs-class.R
Browse code

version 1.9.11

Fix the defunct fasta.info.

Ge Tan authored on 23/06/2016 12:56:19
Showing 1 changed files
NAMESPACE
History View file @ 66144fa
... ... 
@@ -31,7 +31,7 @@ importMethodsFrom(GenomicAlignments, last)
31 31 
 importFrom(GenomeInfoDb, Seqinfo)
32 32 
 importFrom(GenomicRanges, GRanges)
33 33 
 importFrom(GenomicAlignments, explodeCigarOps, CIGAR_OPS, explodeCigarOpLengths)
34 
-importFrom(Biostrings, DNAStringSet, DNA_BASES, fasta.info)
34 
+importFrom(Biostrings, DNAStringSet, DNA_BASES, fasta.seqlengths)
35 35 
 importFrom(RSQLite, SQLite)
36 36 
 importFrom(methods, is, new)
37 37 
 importFrom(rtracklayer, TwoBitFile)
Browse code

Add CNE width distribution plot

Ge Tan authored on 22/06/2016 18:24:03
Showing 1 changed files
NAMESPACE
History View file @ c00e407
... ... 
@@ -48,6 +48,8 @@ importFrom(reshape2, melt)
48 48 
 importFrom(ggplot2, ggplot, aes, aes_q, aes_string, geom_tile, theme_bw,
49 49 
     xlab, ylab, ggtitle,
50 50 
     scale_fill_continuous, geom_text)
51 
+importFrom(poweRlaw, bootstrap_p, estimate_pars, estimate_xmin)
52 
+importFrom("graphics", "lines", "par", "plot", "text")
51 53
52 54 
 ### -----------------------------------------------------------------
53 55 
 ### Export S4 classes defined in CNEr
... ... 
@@ -138,6 +140,9 @@ export(
138 140 
   ## plot.R
139 141 
   CNEDensity,
140 142
143 
+  # CNE-utils.R
144 
+  plotCNEWidth,
145 
+
141 146 
   ## AssemblyStats.R
142 147 
   N50, N90
143 148 
 )
Browse code

add test

Ge Tan authored on 17/06/2016 14:43:15
Showing 1 changed files
NAMESPACE
History View file @ 8e43bce
... ... 
@@ -19,7 +19,7 @@ importMethodsFrom(GenomicRanges, reduce, "strand<-", strand, start, end,
19 19 
 importMethodsFrom(XVector, subseq)
20 20 
 importMethodsFrom(RSQLite, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)
21 21 
 importMethodsFrom(methods, initialize, show)
22 
-importMethodsFrom(Biostrings, mismatchSummary)
22 
+importMethodsFrom(Biostrings, compareStrings)
23 23 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
24 24 
                   showAsCell, extractROWS, mcols, "mcols<-", split, runValue)
25 25 
 importMethodsFrom(IRanges, slice, ranges)
... ... 
@@ -72,7 +72,8 @@ exportMethods(
72 72 
   first, last, grglist, seqinfo, unique,
73 73
74 74 
   ## Axt-methods.R
75 
-  mismatchSummary
75 
+  #  mismatchSummary
76 
+  summary
76 77 
 )
77 78
78 79 
 ### -----------------------------------------------------------------
Browse code

version 1.9.7.

Add the distribution plot of Axt alignments

Ge Tan authored on 17/06/2016 13:15:35
Showing 1 changed files
NAMESPACE
History View file @ 1acc196
... ... 
@@ -1,5 +1,6 @@
1 1 
 useDynLib(CNEr, .registration = TRUE)
2 2 
 import(BiocGenerics)
3 
+
3 4 
 ### -----------------------------------------------------------------
4 5 
 ### Import S4 classes defined in other packages
5 6 
 ###
... ... 
@@ -16,7 +17,7 @@ importMethodsFrom(GenomeInfoDb, seqnames, seqlengths, seqinfo, as.data.frame)
16 17 
 importMethodsFrom(GenomicRanges, reduce, "strand<-", strand, start, end,
17 18 
                                  findOverlaps, coverage, grglist)
18 19 
 importMethodsFrom(XVector, subseq)
19 
-importMethodsFrom(DBI, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)
20 
+importMethodsFrom(RSQLite, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)
20 21 
 importMethodsFrom(methods, initialize, show)
21 22 
 importMethodsFrom(Biostrings, mismatchSummary)
22 23 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
... ... 
@@ -43,6 +44,10 @@ importFrom(tools, file_ext)
43 44 
 importFrom(parallel, mcmapply)
44 45 
 importFrom(utils, download.file, read.table, write.table)
45 46 
 importFrom("stats", "setNames")
47 
+importFrom(reshape2, melt)
48 
+importFrom(ggplot2, ggplot, aes, aes_q, aes_string, geom_tile, theme_bw,
49 
+    xlab, ylab, ggtitle,
50 
+    scale_fill_continuous, geom_text)
46 51
47 52 
 ### -----------------------------------------------------------------
48 53 
 ### Export S4 classes defined in CNEr
... ... 
@@ -146,6 +151,9 @@ exportMethods(
146 151 
   targetSeqs, querySeqs,
147 152 
   symCount,
148 153 
   subAxt,
154 
+
155 
+  ## Axt-methods.R
156 
+  matchDistribution,
149 157
150 158 
   # CNE-class.R
151 159 
   CNE12, CNE21,
... ... 
@@ -158,4 +166,4 @@ exportMethods(
158 166 
   ## ceScan.R
159 167 
   ceScan,
160 168 
   cneMerge
161 
-)
162 169 
\ No newline at end of file
170 
+)
Browse code

version 1.9.5

Clean and fix

Ge Tan authored on 24/05/2016 16:06:02
Showing 1 changed files
NAMESPACE
History View file @ 162d693
... ... 
@@ -127,7 +127,7 @@ export(
127 127 
   makeGRBs,
128 128
129 129 
   ## Ancora.R
130 
-  readAncora,
130 
+  readAncora, readAncoraIntoSQLite,
131 131
132 132 
   ## plot.R
133 133 
   CNEDensity,
Browse code

Finish first round

Ge Tan authored on 23/05/2016 19:15:42
Showing 1 changed files
NAMESPACE
History View file @ bf14859
... ... 
@@ -129,6 +129,9 @@ export(
129 129 
   ## Ancora.R
130 130 
   readAncora,
131 131
132 
+  ## plot.R
133 
+  CNEDensity,
134 
+
132 135 
   ## AssemblyStats.R
133 136 
   N50, N90
134 137 
 )
... ... 
@@ -154,8 +157,5 @@ exportMethods(
154 157
155 158 
   ## ceScan.R
156 159 
   ceScan,
157 
-  cneMerge,
158 
-
159 
-  ## plot.r
160 
-  CNEDensity
160 
+  cneMerge
161 161 
 )
162 162 
\ No newline at end of file
Browse code

update vignette; finishing updating saveCNEToSQLite

Ge Tan authored on 18/05/2016 17:55:59
Showing 1 changed files
NAMESPACE
History View file @ 6d76d89
... ... 
@@ -97,6 +97,7 @@ export(
97 97 
   axtInfo,
98 98 
   writeAxt,
99 99 
   read.rmMask.GRanges,
100 
+  saveCNEToSQLite,
100 101
101 102 
   ## ceScan.R
102 103
... ... 
@@ -154,11 +155,7 @@ exportMethods(
154 155 
   ## ceScan.R
155 156 
   ceScan,
156 157 
   cneMerge,
157 
-
158 
-  ## utils.r
159 
-  saveCNEToSQLite,
160 158
161 159 
   ## plot.r
162 160 
   CNEDensity
163 
-)
164 
-
161 
+)
165 162 
\ No newline at end of file
Browse code

Add the unique for GRangePairs

Ge Tan authored on 17/05/2016 18:10:02
Showing 1 changed files
NAMESPACE
History View file @ 2d6d448
... ... 
@@ -64,7 +64,7 @@ exportMethods(
64 64 
   names, seqnames, "names<-", strand,
65 65
66 66 
   ## GRangePairs-class.R
67 
-  first, last, grglist, seqinfo, swap,
67 
+  first, last, grglist, seqinfo, unique,
68 68
69 69 
   ## Axt-methods.R
70 70 
   mismatchSummary
... ... 
@@ -148,6 +148,9 @@ exportMethods(
148 148 
   thresholds,
149 149 
   CNEMerged, CNEFinal,
150 150
151 
+  # GRangePairs-class.R
152 
+  swap,
153 
+
151 154 
   ## ceScan.R
152 155 
   ceScan,
153 156 
   cneMerge,
Browse code

version 1.9.3

Update makeGRBs

Ge Tan authored on 17/05/2016 17:13:38
Showing 1 changed files
NAMESPACE
History View file @ 3480b22
... ... 
@@ -35,7 +35,7 @@ importFrom(RSQLite, SQLite)
35 35 
 importFrom(methods, is, new)
36 36 
 importFrom(rtracklayer, TwoBitFile)
37 37 
 importFrom(readr, read_tsv)
38 
-importFrom(IRanges, IRanges, IntegerList)
38 
+importFrom(IRanges, IRanges, IntegerList, RleViewsList)
39 39 
 importFrom(S4Vectors, .Call2, queryHits, subjectHits, DataFrame,
40 40 
            normalizeSingleBracketSubscript, normalizeDoubleBracketSubscript,
41 41 
            isTRUEorFALSE, isSingleString)
Browse code

shrink the GRB edges by CNEs

Ge Tan authored on 17/05/2016 16:40:51
Showing 1 changed files
NAMESPACE
History View file @ c260f08
... ... 
@@ -20,7 +20,7 @@ importMethodsFrom(DBI, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)
20 20 
 importMethodsFrom(methods, initialize, show)
21 21 
 importMethodsFrom(Biostrings, mismatchSummary)
22 22 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
23 
-                  showAsCell, extractROWS, mcols, "mcols<-")
23 
+                  showAsCell, extractROWS, mcols, "mcols<-", split, runValue)
24 24 
 importMethodsFrom(IRanges, slice, ranges)
25 25 
 importMethodsFrom(GenomicAlignments, last)
26 26
Browse code

verision 1.9.2.

Add read.rmMask.GRanges function

Ge Tan authored on 13/05/2016 12:07:25
Showing 1 changed files
NAMESPACE
History View file @ 5126139
... ... 
@@ -96,6 +96,7 @@ export(
96 96 
   readAxt,
97 97 
   axtInfo,
98 98 
   writeAxt,
99 
+  read.rmMask.GRanges,
99 100
100 101 
   ## ceScan.R
101 102
Browse code

version 1.7.20

add readAncora

Ge Tan authored on 26/04/2016 16:22:00
Showing 1 changed files
NAMESPACE
History View file @ 52e61d2
... ... 
@@ -124,6 +124,9 @@ export(
124 124 
   ## GRB.R
125 125 
   makeGRBs,
126 126
127 
+  ## Ancora.R
128 
+  readAncora,
129 
+
127 130 
   ## AssemblyStats.R
128 131 
   N50, N90
129 132 
 )
Browse code

Update

Ge Tan authored on 20/04/2016 17:30:04
Showing 1 changed files
NAMESPACE
History View file @ 517d91e
... ... 
@@ -126,7 +126,6 @@ export(
126 126
127 127 
   ## AssemblyStats.R
128 128 
   N50, N90
129 
-
130 129 
 )
131 130
132 131 
 ### -----------------------------------------------------------------
Browse code

ceScan is a S4 method

Ge Tan authored on 20/04/2016 17:11:01
Showing 1 changed files
NAMESPACE
History View file @ 91ddc47
... ... 
@@ -97,9 +97,8 @@ export(
97 97 
   axtInfo,
98 98 
   writeAxt,
99 99
100 
-  ## ceScan.r
101 
-  ceScan,
102 
-  cneMerge,
100 
+  ## ceScan.R
101 
+
103 102 
   blatCNE,
104 103 
   #ceScanOneStep,
105 104
... ... 
@@ -142,11 +141,14 @@ exportMethods(
142 141 
   subAxt,
143 142
144 143 
   # CNE-class.R
145 
-  assembly1, assembly2,
146 144 
   CNE12, CNE21,
147 145 
   thresholds,
148 146 
   CNEMerged, CNEFinal,
149 147
148 
+  ## ceScan.R
149 
+  ceScan,
150 
+  cneMerge,
151 
+
150 152 
   ## utils.r
151 153 
   saveCNEToSQLite,
152 154
Browse code

version 1.7.18

Finish until blatCNE

Ge Tan authored on 20/04/2016 15:41:48
Showing 1 changed files
NAMESPACE
History View file @ 28d8fca
... ... 
@@ -101,7 +101,7 @@ export(
101 101 
   ceScan,
102 102 
   cneMerge,
103 103 
   blatCNE,
104 
-  ceScanOneStep,
104 
+  #ceScanOneStep,
105 105
106 106 
   ## makeGeneDbFromUCSC.r
107 107 
   #supportedUCSCtables,
Browse code

version 1.7.17

Finish cneMerge

Ge Tan authored on 19/04/2016 17:48:04
Showing 1 changed files
NAMESPACE
History View file @ ccf4ea1
... ... 
@@ -35,7 +35,7 @@ importFrom(RSQLite, SQLite)
35 35 
 importFrom(methods, is, new)
36 36 
 importFrom(rtracklayer, TwoBitFile)
37 37 
 importFrom(readr, read_tsv)
38 
-importFrom(IRanges, IRanges)
38 
+importFrom(IRanges, IRanges, IntegerList)
39 39 
 importFrom(S4Vectors, .Call2, queryHits, subjectHits, DataFrame,
40 40 
            normalizeSingleBracketSubscript, normalizeDoubleBracketSubscript,
41 41 
            isTRUEorFALSE, isSingleString)
... ... 
@@ -61,11 +61,10 @@ exportMethods(
61 61 
   ## AllClasses.r
62 62 
   length,
63 63 
   score,
64 
-  nchar,
65 64 
   names, seqnames, "names<-", strand,
66 65
67 66 
   ## GRangePairs-class.R
68 
-  first, last, grglist, seqinfo,
67 
+  first, last, grglist, seqinfo, swap,
69 68
70 69 
   ## Axt-methods.R
71 70 
   mismatchSummary
Browse code

Update CNE-class. Not Finished

Ge Tan authored on 15/04/2016 12:50:38
Showing 1 changed files
NAMESPACE
History View file @ 7f26140
... ... 
@@ -85,12 +85,14 @@ export(
85 85 
   #queryAnnotationSQLite,
86 86 
   fetchChromSizes,
87 87
88 
-  ## AllClasses.r
88 
+  ## Axt-class.R
89 89 
   Axt,
90 
+  ## CNE-class.R
90 91 
   CNE,
92 
+  ## GRangePairs-class.R
91 93 
   GRangePairs,
92 94
93 
-  # io.r
95 
+  # IO-methods.R
94 96 
   readBed,
95 97 
   readAxt,
96 98 
   axtInfo,
... ... 
@@ -134,15 +136,17 @@ export(
134 136 
 ###
135 137
136 138 
 exportMethods(
137 
-  ## AllClasses.r
139 
+  ## Axt-class.R
138 140 
   targetRanges, queryRanges,
139 141 
   targetSeqs, querySeqs,
140 142 
   symCount,
141 143 
   subAxt,
144 
+
145 
+  # CNE-class.R
142 146 
   assembly1, assembly2,
143 
-  CNE1, CNE2,
147 
+  CNE12, CNE21,
144 148 
   thresholds,
145 
-  CNEMerged, CNERepeatsFiltered,
149 
+  CNEMerged, CNEFinal,
146 150
147 151 
   ## utils.r
148 152 
   saveCNEToSQLite,
Browse code

version 1.7.13

Finish GRangePairs.

Ge Tan authored on 12/04/2016 13:27:33
Showing 1 changed files
NAMESPACE
History View file @ 193c5b3
... ... 
@@ -38,7 +38,7 @@ importFrom(readr, read_tsv)
38 38 
 importFrom(IRanges, IRanges)
39 39 
 importFrom(S4Vectors, .Call2, queryHits, subjectHits, DataFrame,
40 40 
            normalizeSingleBracketSubscript, normalizeDoubleBracketSubscript,
41 
-           isTRUEorFALSE)
41 
+           isTRUEorFALSE, isSingleString)
42 42 
 importFrom(tools, file_ext)
43 43 
 importFrom(parallel, mcmapply)
44 44 
 importFrom(utils, download.file, read.table, write.table)
Browse code

version 1.7.12

Finish the coersion of GRangePairs

Ge Tan authored on 11/04/2016 17:55:52
Showing 1 changed files
NAMESPACE
History View file @ df1da12
... ... 
@@ -14,13 +14,13 @@ importClassesFrom(Biostrings, DNAStringSet)
14 14 
 importMethodsFrom(rtracklayer, import.bed)
15 15 
 importMethodsFrom(GenomeInfoDb, seqnames, seqlengths, seqinfo, as.data.frame)
16 16 
 importMethodsFrom(GenomicRanges, reduce, "strand<-", strand, start, end,
17 
-                                 findOverlaps, coverage)
17 
+                                 findOverlaps, coverage, grglist)
18 18 
 importMethodsFrom(XVector, subseq)
19 19 
 importMethodsFrom(DBI, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)
20 20 
 importMethodsFrom(methods, initialize, show)
21 21 
 importMethodsFrom(Biostrings, mismatchSummary)
22 22 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
23 
-                  showAsCell, extractROWS, mcols)
23 
+                  showAsCell, extractROWS, mcols, "mcols<-")
24 24 
 importMethodsFrom(IRanges, slice, ranges)
25 25 
 importMethodsFrom(GenomicAlignments, last)
26 26
... ... 
@@ -57,11 +57,15 @@ exportClasses(Axt,
57 57 
 exportMethods(
58 58 
   "[",
59 59 
   c,
60 
+
60 61 
   ## AllClasses.r
61 62 
   length,
62 63 
   score,
63 64 
   nchar,
64 
-  first, last, names, seqnames, "names<-", strand,
65 
+  names, seqnames, "names<-", strand,
66 
+
67 
+  ## GRangePairs-class.R
68 
+  first, last, grglist, seqinfo,
65 69
66 70 
   ## Axt-methods.R
67 71 
   mismatchSummary
Browse code

Update GRangesPairs

Ge Tan authored on 11/04/2016 16:09:02
Showing 1 changed files
NAMESPACE
History View file @ 33bb6f5
... ... 
@@ -37,7 +37,8 @@ importFrom(rtracklayer, TwoBitFile)
37 37 
 importFrom(readr, read_tsv)
38 38 
 importFrom(IRanges, IRanges)
39 39 
 importFrom(S4Vectors, .Call2, queryHits, subjectHits, DataFrame,
40 
-           normalizeSingleBracketSubscript, normalizeDoubleBracketSubscript)
40 
+           normalizeSingleBracketSubscript, normalizeDoubleBracketSubscript,
41 
+           isTRUEorFALSE)
41 42 
 importFrom(tools, file_ext)
42 43 
 importFrom(parallel, mcmapply)
43 44 
 importFrom(utils, download.file, read.table, write.table)
Browse code

Fix the warning and error

Ge Tan authored on 31/03/2016 19:01:46
Showing 1 changed files
NAMESPACE
History View file @ 919b074
... ... 
@@ -1,5 +1,5 @@
1 1 
 useDynLib(CNEr, .registration = TRUE)
2 
-
2 
+import(BiocGenerics)
3 3 
 ### -----------------------------------------------------------------
4 4 
 ### Import S4 classes defined in other packages
5 5 
 ###
... ... 
@@ -20,8 +20,7 @@ importMethodsFrom(DBI, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)
20 20 
 importMethodsFrom(methods, initialize, show)
21 21 
 importMethodsFrom(Biostrings, mismatchSummary)
22 22 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
23 
-                  showAsCell, extractROWS)
24 
-importMethodsFrom(BiocGenerics, score, setdiff, unlist)
23 
+                  showAsCell, extractROWS, mcols)
25 24 
 importMethodsFrom(IRanges, slice, ranges)
26 25 
 importMethodsFrom(GenomicAlignments, last)
27 26
Browse code

Update

Ge Tan authored on 22/03/2016 19:30:16
Showing 1 changed files
NAMESPACE
History View file @ 22a9a2e
... ... 
@@ -38,7 +38,7 @@ importFrom(rtracklayer, TwoBitFile)
38 38 
 importFrom(readr, read_tsv)
39 39 
 importFrom(IRanges, IRanges)
40 40 
 importFrom(S4Vectors, .Call2, queryHits, subjectHits, DataFrame,
41 
-           normalizeSingleBracketSubscript)
41 
+           normalizeSingleBracketSubscript, normalizeDoubleBracketSubscript)
42 42 
 importFrom(tools, file_ext)
43 43 
 importFrom(parallel, mcmapply)
44 44 
 importFrom(utils, download.file, read.table, write.table)
Browse code

import extractROWS

Ge Tan authored on 17/03/2016 15:40:19
Showing 1 changed files
NAMESPACE
History View file @ 1b9b6de
... ... 
@@ -20,7 +20,7 @@ importMethodsFrom(DBI, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)
20 20 
 importMethodsFrom(methods, initialize, show)
21 21 
 importMethodsFrom(Biostrings, mismatchSummary)
22 22 
 importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
23 
-                  showAsCell)
23 
+                  showAsCell, extractROWS)
24 24 
 importMethodsFrom(BiocGenerics, score, setdiff, unlist)
25 25 
 importMethodsFrom(IRanges, slice, ranges)
26 26 
 importMethodsFrom(GenomicAlignments, last)
Browse code

Add vector method for GRangePairs

Ge Tan authored on 16/03/2016 22:51:09
Showing 1 changed files
NAMESPACE
History View file @ 763a42c
... ... 
@@ -19,7 +19,8 @@ importMethodsFrom(XVector, subseq)
19 19 
 importMethodsFrom(DBI, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)
20 20 
 importMethodsFrom(methods, initialize, show)
21 21 
 importMethodsFrom(Biostrings, mismatchSummary)
22 
-importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first)
22 
+importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first,
23 
+                  showAsCell)
23 24 
 importMethodsFrom(BiocGenerics, score, setdiff, unlist)
24 25 
 importMethodsFrom(IRanges, slice, ranges)
25 26 
 importMethodsFrom(GenomicAlignments, last)
... ... 
@@ -36,7 +37,8 @@ importFrom(methods, is, new)
36 37 
 importFrom(rtracklayer, TwoBitFile)
37 38 
 importFrom(readr, read_tsv)
38 39 
 importFrom(IRanges, IRanges)
39 
-importFrom(S4Vectors, .Call2, queryHits, subjectHits, DataFrame)
40 
+importFrom(S4Vectors, .Call2, queryHits, subjectHits, DataFrame,
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+           normalizeSingleBracketSubscript)
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 importFrom(tools, file_ext)
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 importFrom(parallel, mcmapply)
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 importFrom(utils, download.file, read.table, write.table)
Browse code

version 1.7.10.

Add the GrangePairs class.

Ge Tan authored on 16/03/2016 21:19:06
Showing 1 changed files
NAMESPACE
History View file @ 41c1f91
... ... 
@@ -4,7 +4,9 @@ useDynLib(CNEr, .registration = TRUE)
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 ### Import S4 classes defined in other packages
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 ###
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 importClassesFrom(methods, ANY, character, integer, missing)
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-
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+importClassesFrom(S4Vectors, List, characterORNULL, DataFrame)
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+importClassesFrom(GenomicRanges, GRanges)
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+importClassesFrom(Biostrings, DNAStringSet)
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 ### -----------------------------------------------------------------
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 ### Import S4 methods defined in other packages
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@@ -17,9 +19,10 @@ importMethodsFrom(XVector, subseq)
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 importMethodsFrom(DBI, dbGetQuery, dbConnect, dbDisconnect, dbWriteTable)
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 importMethodsFrom(methods, initialize, show)
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 importMethodsFrom(Biostrings, mismatchSummary)
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-importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS)
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+importMethodsFrom(S4Vectors, Rle, isConstant, runmean, elementNROWS, first)
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 importMethodsFrom(BiocGenerics, score, setdiff, unlist)
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 importMethodsFrom(IRanges, slice, ranges)
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+importMethodsFrom(GenomicAlignments, last)
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 ### -----------------------------------------------------------------
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 ### Import ordinary functions, variables in other packages
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@@ -33,16 +36,18 @@ importFrom(methods, is, new)
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 importFrom(rtracklayer, TwoBitFile)
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 importFrom(readr, read_tsv)
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 importFrom(IRanges, IRanges)
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-importFrom(S4Vectors, .Call2, queryHits, subjectHits)
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+importFrom(S4Vectors, .Call2, queryHits, subjectHits, DataFrame)
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 importFrom(tools, file_ext)
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 importFrom(parallel, mcmapply)
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 importFrom(utils, download.file, read.table, write.table)