1. chromstaR
  2. NAMESPACE
Browse code

replaced class()=='x' with is(,x)

ataudt authored on 29/04/2020 22:16:33
Showing 1 changed files
NAMESPACE
History View file @ 95106ba
... ... 
@@ -49,7 +49,7 @@ import(chromstaRData)
49 49 
 import(doParallel)
50 50 
 import(foreach)
51 51 
 import(ggplot2)
52 
-importFrom(BiocGenerics, "%in%")
52 
+importFrom(BiocGenerics,"%in%")
53 53 
 importFrom(GenomicAlignments,first)
54 54 
 importFrom(GenomicAlignments,readGAlignmentPairs)
55 55 
 importFrom(GenomicAlignments,readGAlignments)
Browse code

The %in% generic is now defined in the BiocGenerics package

Hervé Pagès authored on 03/10/2019 05:54:53
Showing 1 changed files
NAMESPACE
History View file @ 7622f73
... ... 
@@ -49,6 +49,7 @@ import(chromstaRData)
49 49 
 import(doParallel)
50 50 
 import(foreach)
51 51 
 import(ggplot2)
52 
+importFrom(BiocGenerics, "%in%")
52 53 
 importFrom(GenomicAlignments,first)
53 54 
 importFrom(GenomicAlignments,readGAlignmentPairs)
54 55 
 importFrom(GenomicAlignments,readGAlignments)
Browse code

bugfixes in version 1.7.2

ataudt authored on 14/07/2018 13:39:28
Showing 1 changed files
NAMESPACE
History View file @ 0bd289b
... ... 
@@ -59,6 +59,7 @@ importFrom(Rsamtools,indexBam)
59 59 
 importFrom(Rsamtools,scanBamFlag)
60 60 
 importFrom(S4Vectors,Rle)
61 61 
 importFrom(S4Vectors,as.factor)
62 
+importFrom(S4Vectors,endoapply)
62 63 
 importFrom(S4Vectors,queryHits)
63 64 
 importFrom(S4Vectors,runmean)
64 65 
 importFrom(S4Vectors,subjectHits)
Browse code

renamed adjustSensitivity to changeMaxPostCutoff

chakalakka authored on 15/02/2018 10:05:19
Showing 1 changed files
NAMESPACE
History View file @ 0dbcedb
... ... 
@@ -4,13 +4,13 @@ S3method(print,combinedMultiHMM)
4 4 
 S3method(print,multiHMM)
5 5 
 S3method(print,uniHMM)
6 6 
 export(Chromstar)
7 
-export(adjustSensitivity)
8 7 
 export(bin2dec)
9 8 
 export(binReads)
10 9 
 export(callPeaksMultivariate)
11 10 
 export(callPeaksReplicates)
12 11 
 export(callPeaksUnivariate)
13 12 
 export(changeFDR)
13 
+export(changeMaxPostCutoff)
14 14 
 export(changePostCutoff)
15 15 
 export(collapseBins)
16 16 
 export(combineMultivariates)
Browse code

pass check

chakalakka authored on 01/02/2018 11:05:52
Showing 1 changed files
NAMESPACE
History View file @ 85779d1
... ... 
@@ -10,6 +10,7 @@ export(binReads)
10 10 
 export(callPeaksMultivariate)
11 11 
 export(callPeaksReplicates)
12 12 
 export(callPeaksUnivariate)
13 
+export(changeFDR)
13 14 
 export(changePostCutoff)
14 15 
 export(collapseBins)
15 16 
 export(combineMultivariates)
Browse code

peakScore now uniformly distributed between 0 and 1 posterior value

chakalakka authored on 24/11/2017 15:07:49
Showing 1 changed files
NAMESPACE
History View file @ 79e729f
... ... 
@@ -4,12 +4,12 @@ S3method(print,combinedMultiHMM)
4 4 
 S3method(print,multiHMM)
5 5 
 S3method(print,uniHMM)
6 6 
 export(Chromstar)
7 
+export(adjustSensitivity)
7 8 
 export(bin2dec)
8 9 
 export(binReads)
9 10 
 export(callPeaksMultivariate)
10 11 
 export(callPeaksReplicates)
11 12 
 export(callPeaksUnivariate)
12 
-export(changeFDR)
13 13 
 export(changePostCutoff)
14 14 
 export(collapseBins)
15 15 
 export(combineMultivariates)
Browse code

plotGenomeBrowser exported

chakalakka authored on 23/11/2017 10:41:40
Showing 1 changed files
NAMESPACE
History View file @ 6e68bc6
... ... 
@@ -31,6 +31,7 @@ export(plotEnrichCountHeatmap)
31 31 
 export(plotEnrichment)
32 32 
 export(plotExpression)
33 33 
 export(plotFoldEnrichHeatmap)
34 
+export(plotGenomeBrowser)
34 35 
 export(plotHistogram)
35 36 
 export(readBamFileAsGRanges)
36 37 
 export(readBedFileAsGRanges)
Browse code

added importFrom for ecdf

chakalakka authored on 20/07/2017 09:40:10
Showing 1 changed files
NAMESPACE
History View file @ 16dc46f
... ... 
@@ -73,6 +73,7 @@ importFrom(stats,cutree)
73 73 
 importFrom(stats,dist)
74 74 
 importFrom(stats,dnbinom)
75 75 
 importFrom(stats,dnorm)
76 
+importFrom(stats,ecdf)
76 77 
 importFrom(stats,hclust)
77 78 
 importFrom(stats,pnbinom)
78 79 
 importFrom(stats,qnorm)
Browse code

added print methods

chakalakka authored on 02/02/2017 15:41:53
Showing 1 changed files
NAMESPACE
History View file @ ff5d9fe
... ... 
@@ -1,5 +1,8 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+S3method(print,combinedMultiHMM)
4 
+S3method(print,multiHMM)
5 
+S3method(print,uniHMM)
3 6 
 export(Chromstar)
4 7 
 export(bin2dec)
5 8 
 export(binReads)
Browse code

small usability improvements

chakalakka authored on 15/12/2016 12:53:51
Showing 1 changed files
NAMESPACE
History View file @ 20b98ed
... ... 
@@ -59,6 +59,7 @@ importFrom(S4Vectors,runmean)
59 59 
 importFrom(S4Vectors,subjectHits)
60 60 
 importFrom(bamsignals,bamCount)
61 61 
 importFrom(grDevices,col2rgb)
62 
+importFrom(grDevices,rgb2hsv)
62 63 
 importFrom(graphics,hist)
63 64 
 importFrom(methods,as)
64 65 
 importFrom(methods,is)
Browse code

reintroduced simulateMultivariate

chakalakka authored on 16/11/2016 14:28:59
Showing 1 changed files
NAMESPACE
History View file @ 169662b
... ... 
@@ -62,6 +62,7 @@ importFrom(grDevices,col2rgb)
62 62 
 importFrom(graphics,hist)
63 63 
 importFrom(methods,as)
64 64 
 importFrom(methods,is)
65 
+importFrom(mvtnorm,rmvnorm)
65 66 
 importFrom(reshape2,melt)
66 67 
 importFrom(stats,aggregate)
67 68 
 importFrom(stats,cutree)
Browse code

added removeCondition

chakalakka authored on 11/11/2016 10:35:07
Showing 1 changed files
NAMESPACE
History View file @ cfe3b11
... ... 
@@ -32,6 +32,7 @@ export(plotHistogram)
32 32 
 export(readBamFileAsGRanges)
33 33 
 export(readBedFileAsGRanges)
34 34 
 export(readCustomBedFile)
35 
+export(removeCondition)
35 36 
 export(stateBrewer)
36 37 
 export(transitionFrequencies)
37 38 
 export(unis2pseudomulti)
Browse code

bugfix for peaks in changePostCutoff

chakalakka authored on 20/10/2016 09:55:44
Showing 1 changed files
NAMESPACE
History View file @ e53bf26
... ... 
@@ -7,6 +7,7 @@ export(callPeaksMultivariate)
7 7 
 export(callPeaksReplicates)
8 8 
 export(callPeaksUnivariate)
9 9 
 export(changeFDR)
10 
+export(changePostCutoff)
10 11 
 export(collapseBins)
11 12 
 export(combineMultivariates)
12 13 
 export(dec2bin)
Browse code

added peak entry to hmm objects

chakalakka authored on 17/10/2016 15:46:03
Showing 1 changed files
NAMESPACE
History View file @ aa45b85
... ... 
@@ -6,15 +6,14 @@ export(binReads)
6 6 
 export(callPeaksMultivariate)
7 7 
 export(callPeaksReplicates)
8 8 
 export(callPeaksUnivariate)
9 
-export(changePostCutoff)
9 
+export(changeFDR)
10 10 
 export(collapseBins)
11 11 
 export(combineMultivariates)
12 12 
 export(dec2bin)
13 
-export(exportBinnedData)
14 
-export(exportCombinedMultivariate)
13 
+export(exportCombinations)
14 
+export(exportCounts)
15 15 
 export(exportGRangesAsBedFile)
16 
-export(exportMultivariate)
17 
-export(exportUnivariates)
16 
+export(exportPeaks)
18 17 
 export(fixedWidthBins)
19 18 
 export(genomicFrequencies)
20 19 
 export(getCombinations)
Browse code

small usability improvements

chakalakka authored on 13/10/2016 17:30:09
Showing 1 changed files
NAMESPACE
History View file @ 39cfc6e
... ... 
@@ -17,6 +17,7 @@ export(exportMultivariate)
17 17 
 export(exportUnivariates)
18 18 
 export(fixedWidthBins)
19 19 
 export(genomicFrequencies)
20 
+export(getCombinations)
20 21 
 export(getDistinctColors)
21 22 
 export(getStateColors)
22 23 
 export(heatmapCombinations)
Browse code

counts -> RPKM in all export and plotting functions

chakalakka authored on 12/10/2016 16:30:23
Showing 1 changed files
NAMESPACE
History View file @ 6c2d0fa
... ... 
@@ -24,9 +24,9 @@ export(heatmapCountCorrelation)
24 24 
 export(heatmapTransitionProbs)
25 25 
 export(loadHmmsFromFiles)
26 26 
 export(plotEnrichCountHeatmap)
27 
+export(plotEnrichment)
27 28 
 export(plotExpression)
28 29 
 export(plotFoldEnrichHeatmap)
29 
-export(plotFoldEnrichment)
30 30 
 export(plotHistogram)
31 31 
 export(readBamFileAsGRanges)
32 32 
 export(readBedFileAsGRanges)
Browse code

no special characters or spaces in experiment.table

chakalakka authored on 30/06/2016 13:25:52
Showing 1 changed files
NAMESPACE
History View file @ dc24b22
... ... 
@@ -58,6 +58,8 @@ importFrom(S4Vectors,subjectHits)
58 58 
 importFrom(bamsignals,bamCount)
59 59 
 importFrom(grDevices,col2rgb)
60 60 
 importFrom(graphics,hist)
61 
+importFrom(methods,as)
62 
+importFrom(methods,is)
61 63 
 importFrom(reshape2,melt)
62 64 
 importFrom(stats,aggregate)
63 65 
 importFrom(stats,cutree)
Browse code

changed bed -> bam examples

chakalakka authored on 16/06/2016 19:23:58
Showing 1 changed files
NAMESPACE
History View file @ 4c77bd9
... ... 
@@ -28,7 +28,6 @@ export(plotExpression)
28 28 
 export(plotFoldEnrichHeatmap)
29 29 
 export(plotFoldEnrichment)
30 30 
 export(plotHistogram)
31 
-export(plotHistograms)
32 31 
 export(readBamFileAsGRanges)
33 32 
 export(readBedFileAsGRanges)
34 33 
 export(readCustomBedFile)
Browse code

extra speed for BAM files with bamsignals

chakalakka authored on 16/06/2016 16:21:37
Showing 1 changed files
NAMESPACE
History View file @ 26f0862
... ... 
@@ -56,6 +56,7 @@ importFrom(S4Vectors,as.factor)
56 56 
 importFrom(S4Vectors,queryHits)
57 57 
 importFrom(S4Vectors,runmean)
58 58 
 importFrom(S4Vectors,subjectHits)
59 
+importFrom(bamsignals,bamCount)
59 60 
 importFrom(grDevices,col2rgb)
60 61 
 importFrom(graphics,hist)
61 62 
 importFrom(reshape2,melt)
Browse code

please check() with renamed functions

chakalakka authored on 10/06/2016 14:12:53
Showing 1 changed files
NAMESPACE
History View file @ 1a4bfa4
... ... 
@@ -21,6 +21,7 @@ export(getDistinctColors)
21 21 
 export(getStateColors)
22 22 
 export(heatmapCombinations)
23 23 
 export(heatmapCountCorrelation)
24 
+export(heatmapTransitionProbs)
24 25 
 export(loadHmmsFromFiles)
25 26 
 export(plotEnrichCountHeatmap)
26 27 
 export(plotExpression)
... ... 
@@ -28,7 +29,8 @@ export(plotFoldEnrichHeatmap)
28 29 
 export(plotFoldEnrichment)
29 30 
 export(plotHistogram)
30 31 
 export(plotHistograms)
31 
-export(plotTransitionProbs)
32 
+export(readBamFileAsGRanges)
33 
+export(readBedFileAsGRanges)
32 34 
 export(readCustomBedFile)
33 35 
 export(stateBrewer)
34 36 
 export(transitionFrequencies)
Browse code

changed naming of plotting functions

chakalakka authored on 10/06/2016 13:04:00
Showing 1 changed files
NAMESPACE
History View file @ d6704a0
... ... 
@@ -1,12 +1,6 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-S3method(plot,GRanges)
4 
-S3method(plot,character)
5 
-S3method(plot,multiHMM)
6 
-S3method(plot,uniHMM)
7 3 
 export(Chromstar)
8 
-export(bam2GRanges)
9 
-export(bed2GRanges)
10 4 
 export(bin2dec)
11 5 
 export(binReads)
12 6 
 export(callPeaksMultivariate)
... ... 
@@ -18,7 +12,7 @@ export(combineMultivariates)
18 12 
 export(dec2bin)
19 13 
 export(exportBinnedData)
20 14 
 export(exportCombinedMultivariate)
21 
-export(exportGRanges)
15 
+export(exportGRangesAsBedFile)
22 16 
 export(exportMultivariate)
23 17 
 export(exportUnivariates)
24 18 
 export(fixedWidthBins)
... ... 
@@ -26,12 +20,16 @@ export(genomicFrequencies)
26 20 
 export(getDistinctColors)
27 21 
 export(getStateColors)
28 22 
 export(heatmapCombinations)
29 
-export(importBed)
23 
+export(heatmapCountCorrelation)
30 24 
 export(loadHmmsFromFiles)
31 
-export(plotEnrichment)
25 
+export(plotEnrichCountHeatmap)
32 26 
 export(plotExpression)
33 
-export(plotHeatmap)
34 
-export(plotMultipleEnrichment)
27 
+export(plotFoldEnrichHeatmap)
28 
+export(plotFoldEnrichment)
29 
+export(plotHistogram)
30 
+export(plotHistograms)
31 
+export(plotTransitionProbs)
32 
+export(readCustomBedFile)
35 33 
 export(stateBrewer)
36 34 
 export(transitionFrequencies)
37 35 
 export(unis2pseudomulti)
... ... 
@@ -47,10 +45,10 @@ importFrom(GenomicAlignments,first)
47 45 
 importFrom(GenomicAlignments,readGAlignmentPairs)
48 46 
 importFrom(GenomicAlignments,readGAlignments)
49 47 
 importFrom(IRanges,subsetByOverlaps)
48 
+importFrom(Rsamtools,BamFile)
50 49 
 importFrom(Rsamtools,ScanBamParam)
51 50 
 importFrom(Rsamtools,indexBam)
52 51 
 importFrom(Rsamtools,scanBamFlag)
53 
-importFrom(Rsamtools,scanBamHeader)
54 52 
 importFrom(S4Vectors,Rle)
55 53 
 importFrom(S4Vectors,as.factor)
56 54 
 importFrom(S4Vectors,queryHits)
... ... 
@@ -58,7 +56,6 @@ importFrom(S4Vectors,runmean)
58 56 
 importFrom(S4Vectors,subjectHits)
59 57 
 importFrom(grDevices,col2rgb)
60 58 
 importFrom(graphics,hist)
61 
-importFrom(graphics,plot)
62 59 
 importFrom(reshape2,melt)
63 60 
 importFrom(stats,aggregate)
64 61 
 importFrom(stats,cutree)
Browse code

corrected file permissions

chakalakka authored on 08/06/2016 09:00:02
Showing 1 changed files
NAMESPACE
History View file @ bd1f09d
1 1 
old mode 100755
2 2 
new mode 100644
Browse code

fixed seqlengths assign bug, ubuntu reinstall

chakalakka authored on 07/06/2016 09:48:47
Showing 1 changed files
NAMESPACE
History View file @ 7ae641e
1 1 
old mode 100644
2 2 
new mode 100755
Browse code

more input correction bugfixes

chakalakka authored on 17/05/2016 15:29:23
Showing 1 changed files
NAMESPACE
History View file @ 4f2ce7f
... ... 
@@ -51,8 +51,10 @@ importFrom(Rsamtools,ScanBamParam)
51 51 
 importFrom(Rsamtools,indexBam)
52 52 
 importFrom(Rsamtools,scanBamFlag)
53 53 
 importFrom(Rsamtools,scanBamHeader)
54 
+importFrom(S4Vectors,Rle)
54 55 
 importFrom(S4Vectors,as.factor)
55 56 
 importFrom(S4Vectors,queryHits)
57 
+importFrom(S4Vectors,runmean)
56 58 
 importFrom(S4Vectors,subjectHits)
57 59 
 importFrom(grDevices,col2rgb)
58 60 
 importFrom(graphics,hist)
Browse code

parallelized chromosomes in multivariate

chakalakka authored on 15/04/2016 09:38:03
Showing 1 changed files
NAMESPACE
History View file @ 8feb429
... ... 
@@ -28,7 +28,6 @@ export(getStateColors)
28 28 
 export(heatmapCombinations)
29 29 
 export(importBed)
30 30 
 export(loadHmmsFromFiles)
31 
-export(mergeChroms)
32 31 
 export(plotEnrichment)
33 32 
 export(plotExpression)
34 33 
 export(plotHeatmap)
... ... 
@@ -56,8 +55,6 @@ importFrom(S4Vectors,as.factor)
56 55 
 importFrom(S4Vectors,queryHits)
57 56 
 importFrom(S4Vectors,subjectHits)
58 57 
 importFrom(grDevices,col2rgb)
59 
-importFrom(grDevices,dev.off)
60 
-importFrom(grDevices,pdf)
61 58 
 importFrom(graphics,hist)
62 59 
 importFrom(graphics,plot)
63 60 
 importFrom(reshape2,melt)
Browse code

first Bioconductor submit

chakalakka authored on 13/04/2016 13:19:53
Showing 1 changed files
NAMESPACE
History View file @ 3de3e4e
... ... 
@@ -12,7 +12,7 @@ export(binReads)
12 12 
 export(callPeaksMultivariate)
13 13 
 export(callPeaksReplicates)
14 14 
 export(callPeaksUnivariate)
15 
-export(changeFDR)
15 
+export(changePostCutoff)
16 16 
 export(collapseBins)
17 17 
 export(combineMultivariates)
18 18 
 export(dec2bin)
... ... 
@@ -22,7 +22,6 @@ export(exportGRanges)
22 22 
 export(exportMultivariate)
23 23 
 export(exportUnivariates)
24 24 
 export(fixedWidthBins)
25 
-export(foldEnrichment)
26 25 
 export(genomicFrequencies)
27 26 
 export(getDistinctColors)
28 27 
 export(getStateColors)
... ... 
@@ -31,7 +30,9 @@ export(importBed)
31 30 
 export(loadHmmsFromFiles)
32 31 
 export(mergeChroms)
33 32 
 export(plotEnrichment)
33 
+export(plotExpression)
34 34 
 export(plotHeatmap)
35 
+export(plotMultipleEnrichment)
35 36 
 export(stateBrewer)
36 37 
 export(transitionFrequencies)
37 38 
 export(unis2pseudomulti)
... ... 
@@ -39,12 +40,14 @@ export(variableWidthBins)
39 40 
 import(GenomeInfoDb)
40 41 
 import(GenomicRanges)
41 42 
 import(IRanges)
43 
+import(chromstaRData)
42 44 
 import(doParallel)
43 45 
 import(foreach)
44 46 
 import(ggplot2)
45 47 
 importFrom(GenomicAlignments,first)
46 48 
 importFrom(GenomicAlignments,readGAlignmentPairs)
47 49 
 importFrom(GenomicAlignments,readGAlignments)
50 
+importFrom(IRanges,subsetByOverlaps)
48 51 
 importFrom(Rsamtools,ScanBamParam)
49 52 
 importFrom(Rsamtools,indexBam)
50 53 
 importFrom(Rsamtools,scanBamFlag)
Browse code

more examples

chakalakka authored on 12/04/2016 13:51:00
Showing 1 changed files
NAMESPACE
History View file @ 9e923fb
... ... 
@@ -21,7 +21,6 @@ export(exportCombinedMultivariate)
21 21 
 export(exportGRanges)
22 22 
 export(exportMultivariate)
23 23 
 export(exportUnivariates)
24 
-export(expressionOverlap)
25 24 
 export(fixedWidthBins)
26 25 
 export(foldEnrichment)
27 26 
 export(genomicFrequencies)
Browse code

more examples

chakalakka authored on 12/04/2016 13:45:57
Showing 1 changed files
NAMESPACE
History View file @ 30fc26b
... ... 
@@ -21,20 +21,18 @@ export(exportCombinedMultivariate)
21 21 
 export(exportGRanges)
22 22 
 export(exportMultivariate)
23 23 
 export(exportUnivariates)
24 
-export(expressionAtPercentageOverlap)
25 24 
 export(expressionOverlap)
26 25 
 export(fixedWidthBins)
27 26 
 export(foldEnrichment)
28 27 
 export(genomicFrequencies)
29 28 
 export(getDistinctColors)
30 29 
 export(getStateColors)
30 
+export(heatmapCombinations)
31 31 
 export(importBed)
32 32 
 export(loadHmmsFromFiles)
33 33 
 export(mergeChroms)
34 
-export(plotCombinatorialEntropy)
35 34 
 export(plotEnrichment)
36 35 
 export(plotHeatmap)
37 
-export(plotUnivariateKaryogram)
38 36 
 export(stateBrewer)
39 37 
 export(transitionFrequencies)
40 38 
 export(unis2pseudomulti)
... ... 
@@ -60,7 +58,6 @@ importFrom(grDevices,dev.off)
60 58 
 importFrom(grDevices,pdf)
61 59 
 importFrom(graphics,hist)
62 60 
 importFrom(graphics,plot)
63 
-importFrom(gtools,mixedsort)
64 61 
 importFrom(reshape2,melt)
65 62 
 importFrom(stats,aggregate)
66 63 
 importFrom(stats,cutree)
Browse code

70% of BiocCheck done

chakalakka authored on 11/04/2016 16:38:16
Showing 1 changed files
NAMESPACE
History View file @ 1e54520
... ... 
@@ -12,12 +12,8 @@ export(binReads)
12 12 
 export(callPeaksMultivariate)
13 13 
 export(callPeaksReplicates)
14 14 
 export(callPeaksUnivariate)
15 
-export(callPeaksUnivariateAllChr)
16 15 
 export(changeFDR)
17 16 
 export(collapseBins)
18 
-export(combinatorialEntropy)
19 
-export(combinatorialFrequency)
20 
-export(combinatorialStates)
21 17 
 export(combineMultivariates)
22 18 
 export(dec2bin)
23 19 
 export(exportBinnedData)
... ... 
@@ -29,21 +25,17 @@ export(expressionAtPercentageOverlap)
29 25 
 export(expressionOverlap)
30 26 
 export(fixedWidthBins)
31 27 
 export(foldEnrichment)
32 
-export(get.state.colors)
33 
-export(getChromLengths)
28 
+export(genomicFrequencies)
34 29 
 export(getDistinctColors)
30 
+export(getStateColors)
31 
+export(importBed)
35 32 
 export(loadHmmsFromFiles)
36 
-export(loadMultiHmmsFromFiles)
37 33 
 export(mergeChroms)
38 34 
 export(plotCombinatorialEntropy)
39 35 
 export(plotEnrichment)
40 36 
 export(plotHeatmap)
41 37 
 export(plotUnivariateKaryogram)
42 
-export(scanBinsizes)
43 38 
 export(stateBrewer)
44 
-export(subsample)
45 
-export(summarizeDiffPeaks)
46 
-export(summarizePeaks)
47 39 
 export(transitionFrequencies)
48 40 
 export(unis2pseudomulti)
49 41 
 export(variableWidthBins)
... ... 
@@ -53,7 +45,6 @@ import(IRanges)
53 45 
 import(doParallel)
54 46 
 import(foreach)
55 47 
 import(ggplot2)
56 
-importFrom(BiocGenerics,unlist)
57 48 
 importFrom(GenomicAlignments,first)
58 49 
 importFrom(GenomicAlignments,readGAlignmentPairs)
59 50 
 importFrom(GenomicAlignments,readGAlignments)
... ... 
@@ -69,6 +60,7 @@ importFrom(grDevices,dev.off)
69 60 
 importFrom(grDevices,pdf)
70 61 
 importFrom(graphics,hist)
71 62 
 importFrom(graphics,plot)
63 
+importFrom(gtools,mixedsort)
72 64 
 importFrom(reshape2,melt)
73 65 
 importFrom(stats,aggregate)
74 66 
 importFrom(stats,cutree)
Browse code

wrapper function

chakalakka authored on 06/04/2016 14:35:58
Showing 1 changed files
NAMESPACE
History View file @ c57e2d9
... ... 
@@ -4,6 +4,7 @@ S3method(plot,GRanges)
4 4 
 S3method(plot,character)
5 5 
 S3method(plot,multiHMM)
6 6 
 S3method(plot,uniHMM)
7 
+export(Chromstar)
7 8 
 export(bam2GRanges)
8 9 
 export(bed2GRanges)
9 10 
 export(bin2dec)
... ... 
@@ -49,6 +50,8 @@ export(variableWidthBins)
49 50 
 import(GenomeInfoDb)
50 51 
 import(GenomicRanges)
51 52 
 import(IRanges)
53 
+import(doParallel)
54 
+import(foreach)
52 55 
 import(ggplot2)
53 56 
 importFrom(BiocGenerics,unlist)
54 57 
 importFrom(GenomicAlignments,first)
... ... 
@@ -62,6 +65,8 @@ importFrom(S4Vectors,as.factor)
62 65 
 importFrom(S4Vectors,queryHits)
63 66 
 importFrom(S4Vectors,subjectHits)
64 67 
 importFrom(grDevices,col2rgb)
68 
+importFrom(grDevices,dev.off)
69 
+importFrom(grDevices,pdf)
65 70 
 importFrom(graphics,hist)
66 71 
 importFrom(graphics,plot)
67 72 
 importFrom(reshape2,melt)
Browse code

on the way to wrapper

chakalakka authored on 05/04/2016 12:36:21
Showing 1 changed files
NAMESPACE
History View file @ c45eccf
... ... 
@@ -36,6 +36,7 @@ export(loadMultiHmmsFromFiles)
36 36 
 export(mergeChroms)
37 37 
 export(plotCombinatorialEntropy)
38 38 
 export(plotEnrichment)
39 
+export(plotHeatmap)
39 40 
 export(plotUnivariateKaryogram)
40 41 
 export(scanBinsizes)
41 42 
 export(stateBrewer)
Browse code

nice plotEnrichment

chakalakka authored on 04/04/2016 13:41:06
Showing 1 changed files
NAMESPACE
History View file @ 1fb5bce
... ... 
@@ -2,8 +2,8 @@
2 2
3 3 
 S3method(plot,GRanges)
4 4 
 S3method(plot,character)
5 
-S3method(plot,chromstaR_multivariateHMM)
6 
-S3method(plot,chromstaR_univariateHMM)
5 
+S3method(plot,multiHMM)
6 
+S3method(plot,uniHMM)
7 7 
 export(bam2GRanges)
8 8 
 export(bed2GRanges)
9 9 
 export(bin2dec)
... ... 
@@ -19,7 +19,6 @@ export(combinatorialFrequency)
19 19 
 export(combinatorialStates)
20 20 
 export(combineMultivariates)
21 21 
 export(dec2bin)
22 
-export(enrichmentCurve)
23 22 
 export(exportBinnedData)
24 23 
 export(exportCombinedMultivariate)
25 24 
 export(exportGRanges)
... ... 
@@ -36,6 +35,7 @@ export(loadHmmsFromFiles)
36 35 
 export(loadMultiHmmsFromFiles)
37 36 
 export(mergeChroms)
38 37 
 export(plotCombinatorialEntropy)
38 
+export(plotEnrichment)
39 39 
 export(plotUnivariateKaryogram)
40 40 
 export(scanBinsizes)
41 41 
 export(stateBrewer)
... ... 
@@ -49,7 +49,6 @@ import(GenomeInfoDb)
49 49 
 import(GenomicRanges)
50 50 
 import(IRanges)
51 51 
 import(ggplot2)
52 
-import(reshape2)
53 52 
 importFrom(BiocGenerics,unlist)
54 53 
 importFrom(GenomicAlignments,first)
55 54 
 importFrom(GenomicAlignments,readGAlignmentPairs)
... ... 
@@ -64,6 +63,7 @@ importFrom(S4Vectors,subjectHits)
64 63 
 importFrom(grDevices,col2rgb)
65 64 
 importFrom(graphics,hist)
66 65 
 importFrom(graphics,plot)
66 
+importFrom(reshape2,melt)
67 67 
 importFrom(stats,aggregate)
68 68 
 importFrom(stats,cutree)
69 69 
 importFrom(stats,dist)
Browse code

more vignette

chakalakka authored on 01/04/2016 15:12:54
Showing 1 changed files
NAMESPACE
History View file @ 51c70a5
... ... 
@@ -4,14 +4,14 @@ S3method(plot,GRanges)
4 4 
 S3method(plot,character)
5 5 
 S3method(plot,chromstaR_multivariateHMM)
6 6 
 S3method(plot,chromstaR_univariateHMM)
7 
-export(bam2binned)
8 
-export(bed2binned)
9 
-export(bedGraph2binned)
7 
+export(bam2GRanges)
8 
+export(bed2GRanges)
10 9 
 export(bin2dec)
10 
+export(binReads)
11 11 
 export(callPeaksMultivariate)
12 12 
 export(callPeaksReplicates)
13 13 
 export(callPeaksUnivariate)
14 
-export(callPeaksUnivariate2)
14 
+export(callPeaksUnivariateAllChr)
15 15 
 export(changeFDR)
16 16 
 export(collapseBins)
17 17 
 export(combinatorialEntropy)
... ... 
@@ -27,6 +27,7 @@ export(exportMultivariate)
27 27 
 export(exportUnivariates)
28 28 
 export(expressionAtPercentageOverlap)
29 29 
 export(expressionOverlap)
30 
+export(fixedWidthBins)
30 31 
 export(foldEnrichment)
31 32 
 export(get.state.colors)
32 33 
 export(getChromLengths)
... ... 
@@ -43,6 +44,7 @@ export(summarizeDiffPeaks)
43 44 
 export(summarizePeaks)
44 45 
 export(transitionFrequencies)
45 46 
 export(unis2pseudomulti)
47 
+export(variableWidthBins)
46 48 
 import(GenomeInfoDb)
47 49 
 import(GenomicRanges)
48 50 
 import(IRanges)
Browse code

on the way to BiocCheck

chakalakka authored on 30/03/2016 12:09:31
Showing 1 changed files
NAMESPACE
History View file @ 06e7e30
... ... 
@@ -1,4 +1,4 @@
1 
-# Generated by roxygen2 (4.1.1): do not edit by hand
1 
+# Generated by roxygen2: do not edit by hand
2 2
3 3 
 S3method(plot,GRanges)
4 4 
 S3method(plot,character)
... ... 
@@ -43,17 +43,37 @@ export(summarizeDiffPeaks)
43 43 
 export(summarizePeaks)
44 44 
 export(transitionFrequencies)
45 45 
 export(unis2pseudomulti)
46 
-import(BiocGenerics)
46 
+import(GenomeInfoDb)
47 47 
 import(GenomicRanges)
48 48 
 import(IRanges)
49 
-import(S4Vectors)
50 49 
 import(ggplot2)
51 50 
 import(reshape2)
51 
+importFrom(BiocGenerics,unlist)
52 52 
 importFrom(GenomicAlignments,first)
53 
-importFrom(GenomicAlignments,readGAlignmentPairsFromBam)
54 
-importFrom(GenomicAlignments,readGAlignmentsFromBam)
53 
+importFrom(GenomicAlignments,readGAlignmentPairs)
54 
+importFrom(GenomicAlignments,readGAlignments)
55 55 
 importFrom(Rsamtools,ScanBamParam)
56 56 
 importFrom(Rsamtools,indexBam)
57 57 
 importFrom(Rsamtools,scanBamFlag)
58 58 
 importFrom(Rsamtools,scanBamHeader)
59 
-useDynLib(chromstaR)
59 
+importFrom(S4Vectors,as.factor)
60 
+importFrom(S4Vectors,queryHits)
61 
+importFrom(S4Vectors,subjectHits)
62 
+importFrom(grDevices,col2rgb)
63 
+importFrom(graphics,hist)
64 
+importFrom(graphics,plot)
65 
+importFrom(stats,aggregate)
66 
+importFrom(stats,cutree)
67 
+importFrom(stats,dist)
68 
+importFrom(stats,dnbinom)
69 
+importFrom(stats,dnorm)
70 
+importFrom(stats,hclust)
71 
+importFrom(stats,pnbinom)
72 
+importFrom(stats,qnorm)
73 
+importFrom(stats,rbinom)
74 
+importFrom(stats,rnbinom)
75 
+importFrom(stats,runif)
76 
+importFrom(stats,stepfun)
77 
+importFrom(utils,read.table)
78 
+importFrom(utils,write.table)
79 
+useDynLib(chromstaR, .registration = TRUE, .fixes = "")
Browse code

added nice color scheme :)

chakalakka authored on 16/02/2016 10:27:53
Showing 1 changed files
NAMESPACE
History View file @ 9d36f17
... ... 
@@ -30,6 +30,7 @@ export(expressionOverlap)
30 30 
 export(foldEnrichment)
31 31 
 export(get.state.colors)
32 32 
 export(getChromLengths)
33 
+export(getDistinctColors)
33 34 
 export(loadHmmsFromFiles)
34 35 
 export(loadMultiHmmsFromFiles)
35 36 
 export(mergeChroms)
Browse code

forgot help files

chakalakka authored on 10/02/2016 18:36:22
Showing 1 changed files
NAMESPACE
History View file @ 8510a4b
... ... 
@@ -11,6 +11,7 @@ export(bin2dec)
11 11 
 export(callPeaksMultivariate)
12 12 
 export(callPeaksReplicates)
13 13 
 export(callPeaksUnivariate)
14 
+export(callPeaksUnivariate2)
14 15 
 export(changeFDR)
15 16 
 export(collapseBins)
16 17 
 export(combinatorialEntropy)
Browse code

corrected paired end read support for binning

chakalakka authored on 10/02/2016 16:27:54
Showing 1 changed files
NAMESPACE
History View file @ 1c43ec4
... ... 
@@ -41,13 +41,17 @@ export(summarizeDiffPeaks)
41 41 
 export(summarizePeaks)
42 42 
 export(transitionFrequencies)
43 43 
 export(unis2pseudomulti)
44 
-import(BSgenome)
45 44 
 import(BiocGenerics)
46 
-import(GenomicAlignments)
47 45 
 import(GenomicRanges)
48 46 
 import(IRanges)
49 
-import(Rsamtools)
50 47 
 import(S4Vectors)
51 48 
 import(ggplot2)
52 49 
 import(reshape2)
50 
+importFrom(GenomicAlignments,first)
51 
+importFrom(GenomicAlignments,readGAlignmentPairsFromBam)
52 
+importFrom(GenomicAlignments,readGAlignmentsFromBam)
53 
+importFrom(Rsamtools,ScanBamParam)
54 
+importFrom(Rsamtools,indexBam)
55 
+importFrom(Rsamtools,scanBamFlag)
56 
+importFrom(Rsamtools,scanBamHeader)
53 57 
 useDynLib(chromstaR)
Browse code

added export for combined multivariate

chakalakka authored on 10/02/2016 11:57:06
Showing 1 changed files
NAMESPACE
History View file @ 5d322fd
... ... 
@@ -20,6 +20,7 @@ export(combineMultivariates)
20 20 
 export(dec2bin)
21 21 
 export(enrichmentCurve)
22 22 
 export(exportBinnedData)
23 
+export(exportCombinedMultivariate)
23 24 
 export(exportGRanges)
24 25 
 export(exportMultivariate)
25 26 
 export(exportUnivariates)
Browse code

combining multivariates is easy now

chakalakka authored on 09/02/2016 19:11:23
Showing 1 changed files
NAMESPACE
History View file @ 3fa7dc0
... ... 
@@ -16,6 +16,7 @@ export(collapseBins)
16 16 
 export(combinatorialEntropy)
17 17 
 export(combinatorialFrequency)
18 18 
 export(combinatorialStates)
19 
+export(combineMultivariates)
19 20 
 export(dec2bin)
20 21 
 export(enrichmentCurve)
21 22 
 export(exportBinnedData)
Browse code

changed levels of multivariate states to full state space

chakalakka authored on 22/09/2015 14:13:56
Showing 1 changed files
NAMESPACE
History View file @ 9da355f
... ... 
@@ -4,7 +4,6 @@ S3method(plot,GRanges)
4 4 
 S3method(plot,character)
5 5 
 S3method(plot,chromstaR_multivariateHMM)
6 6 
 S3method(plot,chromstaR_univariateHMM)
7 
-export(addCombinations)
8 7 
 export(bam2binned)
9 8 
 export(bed2binned)
10 9 
 export(bedGraph2binned)
... ... 
@@ -15,6 +14,7 @@ export(callPeaksUnivariate)
15 14 
 export(changeFDR)
16 15 
 export(collapseBins)
17 16 
 export(combinatorialEntropy)
17 
+export(combinatorialFrequency)
18 18 
 export(combinatorialStates)
19 19 
 export(dec2bin)
20 20 
 export(enrichmentCurve)
... ... 
@@ -22,6 +22,9 @@ export(exportBinnedData)
22 22 
 export(exportGRanges)
23 23 
 export(exportMultivariate)
24 24 
 export(exportUnivariates)
25 
+export(expressionAtPercentageOverlap)
26 
+export(expressionOverlap)
27 
+export(foldEnrichment)
25 28 
 export(get.state.colors)
26 29 
 export(getChromLengths)
27 30 
 export(loadHmmsFromFiles)
... ... 
@@ -34,6 +37,7 @@ export(stateBrewer)
34 37 
 export(subsample)
35 38 
 export(summarizeDiffPeaks)
36 39 
 export(summarizePeaks)
40 
+export(transitionFrequencies)
37 41 
 export(unis2pseudomulti)
38 42 
 import(BSgenome)
39 43 
 import(BiocGenerics)
Browse code

corrected mergeChroms to handle track posteriors

chakalakka authored on 17/08/2015 15:26:06
Showing 1 changed files
NAMESPACE
History View file @ 2687fe5
... ... 
@@ -26,11 +26,10 @@ export(get.state.colors)
26 26 
 export(getChromLengths)
27 27 
 export(loadHmmsFromFiles)
28 28 
 export(loadMultiHmmsFromFiles)
29 
-export(mergeChromsFromMultivariates)
29 
+export(mergeChroms)
30 30 
 export(plotCombinatorialEntropy)
31 31 
 export(plotUnivariateKaryogram)
32 32 
 export(scanBinsizes)
33 
-export(splitUnivariateIntoChromosomes)
34 33 
 export(stateBrewer)
35 34 
 export(subsample)
36 35 
 export(summarizeDiffPeaks)
Browse code

improved stateBrewer performance, added subsampling

chakalakka authored on 02/06/2015 15:26:39
Showing 1 changed files
NAMESPACE
History View file @ 4be6356
... ... 
@@ -32,6 +32,7 @@ export(plotUnivariateKaryogram)
32 32 
 export(scanBinsizes)
33 33 
 export(splitUnivariateIntoChromosomes)
34 34 
 export(stateBrewer)
35 
+export(subsample)
35 36 
 export(summarizeDiffPeaks)
36 37 
 export(summarizePeaks)
37 38 
 export(unis2pseudomulti)
Browse code

several usability changes and vignette update

chakalakka authored on 28/05/2015 18:56:19
Showing 1 changed files
NAMESPACE
History View file @ dad1a2e
... ... 
@@ -1,14 +1,16 @@
1 
-# Generated by roxygen2 (4.1.0): do not edit by hand
1 
+# Generated by roxygen2 (4.1.1): do not edit by hand
2 2
3 3 
 S3method(plot,GRanges)
4 4 
 S3method(plot,character)
5 5 
 S3method(plot,chromstaR_multivariateHMM)
6 6 
 S3method(plot,chromstaR_univariateHMM)
7 
+export(addCombinations)
7 8 
 export(bam2binned)
8 9 
 export(bed2binned)
9 10 
 export(bedGraph2binned)
10 11 
 export(bin2dec)
11 12 
 export(callPeaksMultivariate)
13 
+export(callPeaksReplicates)
12 14 
 export(callPeaksUnivariate)
13 15 
 export(changeFDR)
14 16 
 export(collapseBins)
... ... 
@@ -20,6 +22,7 @@ export(exportBinnedData)
20 22 
 export(exportGRanges)
21 23 
 export(exportMultivariate)
22 24 
 export(exportUnivariates)
25 
+export(get.state.colors)
23 26 
 export(getChromLengths)
24 27 
 export(loadHmmsFromFiles)
25 28 
 export(loadMultiHmmsFromFiles)
Browse code

corrected help section to pass check()

chakalakka authored on 22/04/2015 07:19:58
Showing 1 changed files
NAMESPACE
History View file @ 264d2e8
... ... 
@@ -15,7 +15,6 @@ export(collapseBins)
15 15 
 export(combinatorialEntropy)
16 16 
 export(combinatorialStates)
17 17 
 export(dec2bin)
18 
-export(dzinbinom)
19 18 
 export(enrichmentCurve)
20 19 
 export(exportBinnedData)
21 20 
 export(exportGRanges)
... ... 
@@ -27,9 +26,6 @@ export(loadMultiHmmsFromFiles)
27 26 
 export(mergeChromsFromMultivariates)
28 27 
 export(plotCombinatorialEntropy)
29 28 
 export(plotUnivariateKaryogram)
30 
-export(pzinbinom)
31 
-export(qzinbinom)
32 
-export(rzinbinom)
33 29 
 export(scanBinsizes)
34 30 
 export(splitUnivariateIntoChromosomes)
35 31 
 export(stateBrewer)
... ... 
@@ -42,6 +38,7 @@ import(GenomicAlignments)
42 38 
 import(GenomicRanges)
43 39 
 import(IRanges)
44 40 
 import(Rsamtools)
41 
+import(S4Vectors)
45 42 
 import(ggplot2)
46 43 
 import(reshape2)
47 44 
 useDynLib(chromstaR)
Browse code

bugfixes and improvements

chakalakka authored on 31/03/2015 08:09:49
Showing 1 changed files
NAMESPACE
History View file @ a726763
... ... 
@@ -1,6 +1,7 @@
1 1 
 # Generated by roxygen2 (4.1.0): do not edit by hand
2 2
3 3 
 S3method(plot,GRanges)
4 
+S3method(plot,character)
4 5 
 S3method(plot,chromstaR_multivariateHMM)
5 6 
 S3method(plot,chromstaR_univariateHMM)
6 7 
 export(bam2binned)
... ... 
@@ -15,6 +16,7 @@ export(combinatorialEntropy)
15 16 
 export(combinatorialStates)
16 17 
 export(dec2bin)
17 18 
 export(dzinbinom)
19 
+export(enrichmentCurve)
18 20 
 export(exportBinnedData)
19 21 
 export(exportGRanges)
20 22 
 export(exportMultivariate)
Browse code

bugfix in posteriors per track, several small improvements

chakalakka authored on 05/03/2015 16:42:28
Showing 1 changed files
NAMESPACE
History View file @ 36ce9e8
... ... 
@@ -16,6 +16,7 @@ export(combinatorialStates)
16 16 
 export(dec2bin)
17 17 
 export(dzinbinom)
18 18 
 export(exportBinnedData)
19 
+export(exportGRanges)
19 20 
 export(exportMultivariate)
20 21 
 export(exportUnivariates)
21 22 
 export(getChromLengths)
... ... 
@@ -23,6 +24,7 @@ export(loadHmmsFromFiles)
23 24 
 export(loadMultiHmmsFromFiles)
24 25 
 export(mergeChromsFromMultivariates)
25 26 
 export(plotCombinatorialEntropy)
27 
+export(plotUnivariateKaryogram)
26 28 
 export(pzinbinom)
27 29 
 export(qzinbinom)
28 30 
 export(rzinbinom)
Browse code

added combinatorial entropy

chakalakka authored on 26/02/2015 19:23:52
Showing 1 changed files
NAMESPACE
History View file @ 6bbda0e
... ... 
@@ -11,6 +11,7 @@ export(callPeaksMultivariate)
11 11 
 export(callPeaksUnivariate)
12 12 
 export(changeFDR)
13 13 
 export(collapseBins)
14 
+export(combinatorialEntropy)
14 15 
 export(combinatorialStates)
15 16 
 export(dec2bin)
16 17 
 export(dzinbinom)
... ... 
@@ -21,6 +22,7 @@ export(getChromLengths)
21 22 
 export(loadHmmsFromFiles)
22 23 
 export(loadMultiHmmsFromFiles)
23 24 
 export(mergeChromsFromMultivariates)
25 
+export(plotCombinatorialEntropy)
24 26 
 export(pzinbinom)
25 27 
 export(qzinbinom)
26 28 
 export(rzinbinom)
... ... 
@@ -31,6 +33,7 @@ export(summarizeDiffPeaks)
31 33 
 export(summarizePeaks)
32 34 
 export(unis2pseudomulti)
33 35 
 import(BSgenome)
36 
+import(BiocGenerics)
34 37 
 import(GenomicAlignments)
35 38 
 import(GenomicRanges)
36 39 
 import(IRanges)
Browse code

passing check()

chakalakka authored on 23/02/2015 12:31:31
Showing 1 changed files
NAMESPACE
History View file @ 152af28
... ... 
@@ -30,6 +30,7 @@ export(stateBrewer)
30 30 
 export(summarizeDiffPeaks)
31 31 
 export(summarizePeaks)
32 32 
 export(unis2pseudomulti)
33 
+import(BSgenome)
33 34 
 import(GenomicAlignments)
34 35 
 import(GenomicRanges)
35 36 
 import(IRanges)
Browse code

roxygenized documentation

chakalakka authored on 23/02/2015 11:54:03
Showing 1 changed files
NAMESPACE
History View file @ 04140bd
... ... 
@@ -1,72 +1,39 @@
1 
+# Generated by roxygen2 (4.1.0): do not edit by hand
2 
+
3 
+S3method(plot,GRanges)
4 
+S3method(plot,chromstaR_multivariateHMM)
5 
+S3method(plot,chromstaR_univariateHMM)
6 
+export(bam2binned)
7 
+export(bed2binned)
8 
+export(bedGraph2binned)
9 
+export(bin2dec)
10 
+export(callPeaksMultivariate)
11 
+export(callPeaksUnivariate)
12 
+export(changeFDR)
13 
+export(collapseBins)
14 
+export(combinatorialStates)
15 
+export(dec2bin)
16 
+export(dzinbinom)
17 
+export(exportBinnedData)
18 
+export(exportMultivariate)
19 
+export(exportUnivariates)
20 
+export(getChromLengths)
21 
+export(loadHmmsFromFiles)
22 
+export(loadMultiHmmsFromFiles)
23 
+export(mergeChromsFromMultivariates)
24 
+export(pzinbinom)
25 
+export(qzinbinom)
26 
+export(rzinbinom)
27 
+export(scanBinsizes)
28 
+export(splitUnivariateIntoChromosomes)
29 
+export(stateBrewer)
30 
+export(summarizeDiffPeaks)
31 
+export(summarizePeaks)
32 
+export(unis2pseudomulti)
33 
+import(GenomicAlignments)
34 
+import(GenomicRanges)
35 
+import(IRanges)
36 
+import(Rsamtools)
37 
+import(ggplot2)
38 
+import(reshape2)
1 39 
 useDynLib(chromstaR)
2 
-
3 
-S3method(plot, chromstaR_univariateHMM)
4 
-S3method(plot, chromstaR_multivariateHMM)
5 
-
6 
-# Export all names
7 
-# exportPattern(".")
8 
-export(
9 
-bed2binned,
10 
-bam2binned,
11 
-bedGraph2binned,
12 
-# get.chrom.lengths,
13 
-
14 
-callPeaksUnivariate,
15 
-# prepare.multivariate,
16 
-callPeaksMultivariate,
17 
-unis2pseudomulti,
18 
-splitUnivariateIntoChromosomes,
19 
-mergeChromsFromMultivariates,
20 
-loadHmmsFromFiles,
21 
-loadMultiHmmsFromFiles,