| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: chromstaR |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data |
| 4 |
-Version: 1.11.0 |
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| 4 |
+Version: 1.11.1 |
|
| 5 | 5 |
Author: Aaron Taudt, Maria Colome Tatche, Matthias Heinig, Minh Anh Nguyen |
| 6 | 6 |
Maintainer: Aaron Taudt <aaron.taudt@gmail.com> |
| 7 | 7 |
Description: This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses. |
| ... | ... |
@@ -193,30 +193,32 @@ exportUnivariatePeaks <- function(hmm.list, filename, header=TRUE, separate.file |
| 193 | 193 |
} |
| 194 | 194 |
cat(paste0("track name=\"",trackname.string,"\" description=\"",trackname.string,"\" visibility=1 itemRgb=Off priority=",priority,"\n"), file=filename.gz, append=TRUE)
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| 195 | 195 |
} |
| 196 |
- if (is.null(peaks$maxPostInPeak)) {
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| 197 |
- peaks$peakScores <- 0 |
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| 198 |
- } else {
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| 199 |
- peaks$peakScores <- suppressWarnings( -10*log10(1-peaks$maxPostInPeak) ) |
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| 200 |
- peaks$peakScores[is.nan(peaks$peakScores) | peaks$peakScores > 1000] <- 1000 |
|
| 201 |
- } |
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| 202 |
- df <- as.data.frame(peaks) |
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| 203 |
- df$peakNumber <- paste0('peak_', 1:nrow(df))
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| 204 |
- df$strand <- sub('\\*', '.', df$strand)
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| 205 |
- df <- df[,c('chromosome','start','end','peakNumber','peakScores','strand')]
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| 206 |
- # Make score integer |
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| 207 |
- df$peakScores <- round(df$peakScores) |
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| 208 |
- numsegments <- nrow(df) |
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| 209 |
- # Convert from 1-based closed to 0-based half open |
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| 210 |
- df$start <- df$start - 1 |
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| 211 |
- # df$thickStart <- df$start |
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| 212 |
- # df$thickEnd <- df$end |
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| 213 |
- # # Colors |
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| 214 |
- # RGB <- t(grDevices::col2rgb(getStateColors('modified')))
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| 215 |
- # df$itemRgb <- apply(RGB,1,paste,collapse=",") |
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| 216 |
- if (nrow(df) == 0) {
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| 217 |
- warning('hmm ',imod,' does not contain any \'modified\' calls')
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| 218 |
- } else {
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| 219 |
- utils::write.table(format(df, scientific=FALSE, trim=TRUE), file=filename.gz, append=TRUE, row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t') |
|
| 196 |
+ if (length(peaks) > 0) {
|
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| 197 |
+ if (is.null(peaks$maxPostInPeak)) {
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| 198 |
+ peaks$peakScores <- 0 |
|
| 199 |
+ } else {
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|
| 200 |
+ peaks$peakScores <- suppressWarnings( -10*log10(1-peaks$maxPostInPeak) ) |
|
| 201 |
+ peaks$peakScores[is.nan(peaks$peakScores) | peaks$peakScores > 1000] <- 1000 |
|
| 202 |
+ } |
|
| 203 |
+ df <- as.data.frame(peaks) |
|
| 204 |
+ df$peakNumber <- paste0('peak_', 1:nrow(df))
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| 205 |
+ df$strand <- sub('\\*', '.', df$strand)
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| 206 |
+ df <- df[,c('chromosome','start','end','peakNumber','peakScores','strand')]
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|
| 207 |
+ # Make score integer |
|
| 208 |
+ df$peakScores <- round(df$peakScores) |
|
| 209 |
+ numsegments <- nrow(df) |
|
| 210 |
+ # Convert from 1-based closed to 0-based half open |
|
| 211 |
+ df$start <- df$start - 1 |
|
| 212 |
+ # df$thickStart <- df$start |
|
| 213 |
+ # df$thickEnd <- df$end |
|
| 214 |
+ # # Colors |
|
| 215 |
+ # RGB <- t(grDevices::col2rgb(getStateColors('modified')))
|
|
| 216 |
+ # df$itemRgb <- apply(RGB,1,paste,collapse=",") |
|
| 217 |
+ if (nrow(df) == 0) {
|
|
| 218 |
+ warning('hmm ',imod,' does not contain any \'modified\' calls')
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|
| 219 |
+ } else {
|
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| 220 |
+ utils::write.table(format(df, scientific=FALSE, trim=TRUE), file=filename.gz, append=TRUE, row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t') |
|
| 221 |
+ } |
|
| 220 | 222 |
} |
| 221 | 223 |
if (separate.files) {
|
| 222 | 224 |
close(filename.gz) |
