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‎DESCRIPTION‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,14 @@
11
Package: permseq
22
Type: Package
3-
Title: Mapping protein-DNA interactions in highly repetitive regions of the genomes with prior-enhanced read mapping.
4-
Version: 0.99.0
5-
Date: 2015-03-18
3+
Title: Mapping protein-DNA interactions in highly repetitive regions of the genomes with prior-enhanced read mapping
4+
Version: 0.2.0
5+
Date: 2016-11-01
66
Author: Xin Zeng, M. Constanza Rojo-Alfaro, Ye Zheng, Sunduz Keles
7-
Maintainer: Xin Zeng <xinzeng@stat.wisc.edu>, M. Constanza Rojo-Alfaro <rojo@stat.wisc.edu>, Ye Zheng <yezheng@stat.wisc.edu>
7+
Maintainer: Ye Zheng <yezheng@stat.wisc.edu>, M. Constanza Rojo-Alfaro <[email protected]>
88
Description: Multi-reads allocation of ChIP-seq data.
99
License: GPL (>= 2)
10-
Depends: R (>= 2.12.0), MASS, splines, parallel, grplasso, methods
10+
Depends: R (>= 3.1.0), MASS, grplasso, methods
1111
LazyLoad: yes
12-
biocViews: ChIPseq, Sequencing, Transcription, multi-read
12+
biocViews: ChIPseq, Sequencing, Transcription, Multi-read
1313
SystemRequirements: Perl
1414
Suggests: knitr

‎DESCRIPTION~‎

Lines changed: 14 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,14 @@
1+
Package: permseq
2+
Type: Package
3+
Title: Mapping protein-DNA interactions in highly repetitive regions of the genomes with prior-enhanced read mapping
4+
Version: 0.2.0
5+
Date: 2016-08-19
6+
Author: Xin Zeng, M. Constanza Rojo-Alfaro, Ye Zheng, Sunduz Keles
7+
Maintainer: Ye Zheng <[email protected]>, M. Constanza Rojo-Alfaro <[email protected]>
8+
Description: Multi-reads allocation of ChIP-seq data.
9+
License: GPL (>= 2)
10+
Depends: R (>= 3.1.0), MASS, grplasso, methods
11+
LazyLoad: yes
12+
biocViews: ChIPseq, Sequencing, Transcription, Multi-read
13+
SystemRequirements: Perl
14+
Suggests: knitr

‎NAMESPACE~‎

Lines changed: 18 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,18 @@
1+
# Generated by roxygen2 (4.1.0): do not edit by hand
2+
3+
export(priorGenerate)
4+
export(priorProcess)
5+
export(priorHistone_init)
6+
export(priorHistone_multi)
7+
export(readAllocate)
8+
export(plot)
9+
export(print)
10+
export(summary)
11+
exportMethods("plot")
12+
exportMethods("summary")
13+
exportMethods("print")
14+
import(MASS)
15+
import(grplasso)
16+
import(methods)
17+
import(parallel)
18+
import(spline)

‎R/base_chipMeanCounts.R‎

Lines changed: 18 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -1,43 +1,32 @@
1-
.chipMeanCounts=function(prior = NULL, position_cluster,ChipSamFileLoc,ChipSamFile,OutfileLoc="./",Outfile){
1+
.chipMeanCounts = function(prior = NULL, position_cluster, chipSAM, ChipSamFile, OutfileLoc="./", Outfile){
22
setwd(OutfileLoc)
33

4-
if(length(prior) != 0){ #if there is an existing "Prior" object
5-
if(length(prior[['chipUni']] == 0)){#if the uni_bed file is not available now
4+
if(length(prior[['chipUni']] == 0)){#if the uni_bed file is not available now
65
# Obtain uni-reads from each ChIP file
7-
for(i in 1:length(ChipSamFile)){
8-
ChipUniFile=paste(ChipSamFile[i],'.uni.bed',sep='')
9-
script='find_uni_bed.pl'
10-
Fn.Path <- system.file( file.path("Perl",script), package="permseq")
11-
CMD<-paste('perl ',Fn.Path,' ', ChipSamFileLoc[i],'/',ChipSamFile[i],' ', OutfileLoc,'/',ChipUniFile,sep='')
12-
system(CMD,intern=TRUE)
13-
}
14-
}
15-
}
16-
else{
176
for(i in 1:length(ChipSamFile)){
18-
ChipUniFile=paste(ChipSamFile[i],'.uni.bed',sep='')
19-
script='find_uni_bed.pl'
20-
Fn.Path <- system.file( file.path("Perl",script), package="permseq")
21-
CMD<-paste('perl ',Fn.Path,' ', ChipSamFileLoc[i],'/',ChipSamFile[i],' ', OutfileLoc,'/',ChipUniFile,sep='')
22-
system(CMD,intern=TRUE)
23-
}
7+
ChipUniFile <- paste(ChipSamFile[i], '.uni.bed', sep='')
8+
script <- 'find_uni_bed.pl'
9+
Fn.Path <- system.file(file.path("Perl", script), package="permseq")
10+
CMD <- paste('perl ', Fn.Path, ' ', chipSAM, ' ', OutfileLoc, '/', ChipUniFile, sep='')
11+
system(CMD, intern=TRUE)
12+
}
2413
}
25-
# Obtain ChIP mean counts for each data
14+
# Obtain ChIP mean counts for each data
2615
for(j in 1:length(position_cluster)){
27-
CMD='cat '
16+
CMD <- 'cat '
2817
for(l in 1:length(position_cluster[[j]])){
29-
CMD=paste(CMD,position_cluster[[j]][[l]],sep=' ')
18+
CMD <- paste(CMD, position_cluster[[j]][[l]], sep=' ')
3019
}
31-
CMD=paste(CMD,'>cluster_temp.txt',sep='')
20+
CMD <- paste(CMD, '>cluster_temp.txt', sep='')
3221
system(CMD)
33-
# Calculate averaged ChIP counts at different read counts
34-
script='mean_chip_update.pl'
35-
Fn.Path <- system.file( file.path("Perl",script), package="permseq")
22+
# Calculate averaged ChIP counts at different read counts
23+
script <- 'mean_chip_update.pl'
24+
Fn.Path <- system.file(file.path("Perl", script), package="permseq")
3625

3726
for(i in 1:length(ChipSamFile)){
38-
ChipUniFile=paste(ChipSamFile[i],'.uni.bed',sep='')
39-
system(paste('rm -rf ',OutfileLoc,'/',names(position_cluster)[j],'_',Outfile[i],'.txt',sep='') )
40-
CMD<-paste('perl ',Fn.Path,' ', OutfileLoc,'/',ChipUniFile, ' ','cluster_temp.txt',' ', OutfileLoc,'/', names(position_cluster)[j],'_',Outfile[i],sep='')
27+
ChipUniFile <- paste(ChipSamFile[i], '.uni.bed', sep='')
28+
system(paste('rm -rf ', OutfileLoc, '/', names(position_cluster)[j], '_', Outfile[i], '.txt', sep='') )
29+
CMD <- paste('perl ', Fn.Path, ' ', OutfileLoc, '/', ChipUniFile, ' ', 'cluster_temp.txt', ' ', OutfileLoc, '/', names(position_cluster)[j], '_', Outfile[i], sep='')
4130
system(CMD,intern=TRUE)
4231
}
4332
system('rm -rf cluster_temp.txt')

‎R/base_chipMeanCounts_multi.R‎

Lines changed: 28 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -1,49 +1,49 @@
1-
.chipMeanCounts_multi=function(priorObject,OutfileLoc="./",Outfile){
1+
.chipMeanCounts_multi = function(priorObject, OutfileLoc="./", Outfile){
22

33
setwd(OutfileLoc)
4-
ChipSamFile=NULL
4+
ChipSamFile <- NULL
55
for(i in 1:length(priorObject[['chipSAM']])){
6-
temp=strsplit(as.character(priorObject[['chipSAM']][i]),'/')[[1]]
7-
ChipSamFile=c(ChipSamFile,temp[length(temp)])
6+
temp <- strsplit(as.character(priorObject[['chipSAM']][i]), '/')[[1]]
7+
ChipSamFile <- c(ChipSamFile, temp[length(temp)])
88
}
99
#if no uni-reads from sam have been extracted:
1010
if(length(priorObject[['chipUni']]) == 0){
1111
for(i in 1:length(ChipSamFile)){
12-
ChipUniFile=paste(ChipSamFile[i],'.uni.bed',sep='')
13-
priorObject[['chipUni']]=c(priorObject[['chipUni']],paste(OutfileLoc,'/',ChipUniFile,sep=''))
12+
ChipUniFile <- paste(ChipSamFile[i], '.uni.bed', sep='')
13+
priorObject[['chipUni']] <- c(priorObject[['chipUni']], paste(OutfileLoc, '/', ChipUniFile, sep=''))
1414
# Convert SAM to uni-reads BED format
15-
script='find_uni_bed.pl'
16-
Fn.Path <- system.file( file.path("Perl",script), package="permseq")
17-
CMD<-paste('perl ',Fn.Path,' ', priorObject[['chipSAM']][[i]],' ', OutfileLoc,'/',ChipUniFile,sep='')
18-
system(CMD,intern=TRUE)
15+
script <- 'find_uni_bed.pl'
16+
Fn.Path <- system.file(file.path("Perl", script), package="permseq")
17+
CMD <- paste('perl ', Fn.Path, ' ', priorObject[['chipSAM']][[i]], ' ', OutfileLoc, '/', ChipUniFile, sep='')
18+
system(CMD, intern=TRUE)
1919
}
2020
}
2121

2222
for(i in 1:length(ChipSamFile)){
2323
# Count number of reads aligned to each nucleotide
24-
script='count_tags_at_each_nucleotide.pl'
25-
Fn.Path <- system.file( file.path("Perl",script), package="permseq")
26-
ChipUniFile=priorObject[['chipUni']][i]
27-
ChipUniFileN=strsplit(ChipUniFile,'/')[[1]]
28-
ChipUniFileN=ChipUniFileN[length(ChipUniFileN)]
29-
ChipUniCountFile=paste(OutfileLoc,'/',ChipUniFileN,'_count.txt_temp',sep='')
30-
CMD<-paste('perl ',Fn.Path,' ', ChipUniFile,' ',ChipUniCountFile,sep='')
31-
system(CMD,intern=TRUE)
24+
script <- 'count_tags_at_each_nucleotide.pl'
25+
Fn.Path <- system.file( file.path("Perl", script), package="permseq")
26+
ChipUniFile <- priorObject[['chipUni']][i]
27+
ChipUniFileN <- strsplit(ChipUniFile, '/')[[1]]
28+
ChipUniFileN <- ChipUniFileN[length(ChipUniFileN)]
29+
ChipUniCountFile <- paste(OutfileLoc, '/', ChipUniFileN, '_count.txt_temp', sep='')
30+
CMD <- paste('perl ', Fn.Path, ' ', ChipUniFile, ' ', ChipUniCountFile, sep='')
31+
system(CMD, intern=TRUE)
3232
#split countfiles
3333
setwd(OutfileLoc)
34-
outfileLoc=fileDir="./"
35-
file=strsplit(ChipUniCountFile,'/')[[1]]
36-
file=file[length(file)]
37-
system( paste("awk -F \"\\t\" \'{close(f);f=$1}{print > \"",dirname(outfileLoc),"/",basename(outfileLoc), paste("/","/\"f\"",'_',file,"\"}\' ",sep=''),fileDir,file,sep=""))
34+
outfileLoc <- fileDir <- "./"
35+
file <- strsplit(ChipUniCountFile, '/')[[1]]
36+
file <- file[length(file)]
37+
system( paste("awk -F \"\\t\" \'{close(f);f=$1}{print > \"", dirname(outfileLoc), "/", basename(outfileLoc), paste("/", "/\"f\"", '_', file, "\"}\' ", sep=''), fileDir, file, sep=""))
3838

3939
# Calculate average of ChIP read counts for each group defined by "posLoc_bychr"
40-
script='mean_chip_multidata.pl'
41-
Fn.Path <- system.file( file.path("Perl",script), package="permseq")
42-
chrlist=names(priorObject[['posLoc_bychr']])
40+
script <- 'mean_chip_multidata.pl'
41+
Fn.Path <- system.file(file.path("Perl", script), package="permseq")
42+
chrlist <- names(priorObject[['posLoc_bychr']])
4343
for(chr in chrlist){
44-
system(paste('rm -rf ',outfileLoc,'/',chr,'_',Outfile[i],sep=''))
45-
CMD<-paste('perl ',Fn.Path,' ', chr,'_',file,' ',priorObject[['posLoc_bychr']][[chr]],' ',paste(outfileLoc,'/',chr,'_',Outfile[i],sep=''),' ',priorObject[['dataNum']],sep='')
46-
system(CMD,intern=TRUE)
44+
system(paste('rm -rf ', outfileLoc, '/', chr, '_', Outfile[i], sep=''))
45+
CMD <- paste('perl ', Fn.Path,' ', chr, '_', file, ' ', priorObject[['posLoc_bychr']][[chr]], ' ', paste(outfileLoc, '/', chr, '_', Outfile[i], sep=''), ' ', priorObject[['dataNum']], sep='')
46+
system(CMD, intern=TRUE)
4747
}
4848
}
4949
return(priorObject)

‎R/base_chipMeanCounts_multi.R~‎

Lines changed: 50 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,50 @@
1+
.chipMeanCounts_multi = function(priorObject, OutfileLoc="./", Outfile){
2+
3+
setwd(OutfileLoc)
4+
ChipSamFile <- NULL
5+
for(i in 1:length(priorObject[['chipSAM']])){
6+
temp <- strsplit(as.character(priorObject[['chipSAM']][i]), '/')[[1]]
7+
ChipSamFile <- c(ChipSamFile, temp[length(temp)])
8+
}
9+
#if no uni-reads from sam have been extracted:
10+
if(length(priorObject[['chipUni']]) == 0){
11+
for(i in 1:length(ChipSamFile)){
12+
ChipUniFile <- paste(ChipSamFile[i], '.uni.bed', sep='')
13+
priorObject[['chipUni']] <- c(priorObject[['chipUni']], paste(OutfileLoc, '/', ChipUniFile, sep=''))
14+
# Convert SAM to uni-reads BED format
15+
#script <- 'find_uni_bed.pl'
16+
#Fn.Path <- system.file(file.path("Perl", script), package="permseq")
17+
#CMD <- paste('perl ', Fn.Path, ' ', priorObject[['chipSAM']][[i]], ' ', OutfileLoc, '/', ChipUniFile, sep='')
18+
#system(CMD, intern=TRUE)
19+
}
20+
}
21+
22+
for(i in 1:length(ChipSamFile)){
23+
# Count number of reads aligned to each nucleotide
24+
script <- 'count_tags_at_each_nucleotide.pl'
25+
Fn.Path <- system.file( file.path("Perl", script), package="permseq")
26+
ChipUniFile <- priorObject[['chipUni']][i]
27+
ChipUniFileN <- strsplit(ChipUniFile, '/')[[1]]
28+
ChipUniFileN <- ChipUniFileN[length(ChipUniFileN)]
29+
ChipUniCountFile <- paste(OutfileLoc, '/', ChipUniFileN, '_count.txt_temp', sep='')
30+
CMD <- paste('perl ', Fn.Path, ' ', ChipUniFile, ' ', ChipUniCountFile, sep='')
31+
system(CMD, intern=TRUE)
32+
#split countfiles
33+
setwd(OutfileLoc)
34+
outfileLoc <- fileDir <- "./"
35+
file <- strsplit(ChipUniCountFile, '/')[[1]]
36+
file <- file[length(file)]
37+
system( paste("awk -F \"\\t\" \'{close(f);f=$1}{print > \"", dirname(outfileLoc), "/", basename(outfileLoc), paste("/", "/\"f\"", '_', file, "\"}\' ", sep=''), fileDir, file, sep=""))
38+
39+
# Calculate average of ChIP read counts for each group defined by "posLoc_bychr"
40+
script <- 'mean_chip_multidata.pl'
41+
Fn.Path <- system.file(file.path("Perl", script), package="permseq")
42+
chrlist <- names(priorObject[['posLoc_bychr']])
43+
for(chr in chrlist){
44+
system(paste('rm -rf ', outfileLoc, '/', chr, '_', Outfile[i], sep=''))
45+
CMD <- paste('perl ', Fn.Path,' ', chr, '_', file, ' ', priorObject[['posLoc_bychr']][[chr]], ' ', paste(outfileLoc, '/', chr, '_', Outfile[i], sep=''), ' ', priorObject[['dataNum']], sep='')
46+
system(CMD, intern=TRUE)
47+
}
48+
}
49+
return(priorObject)
50+
}

‎R/base_clusterPositions.R‎

Lines changed: 20 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1,39 +1,39 @@
1-
.clusterPositions=function(countFile,chrList,outfileLoc="./" ,chrom.ref,outfile){
1+
.clusterPositions = function(countFile, chrList, outfileLoc="./", chrom.ref, outfile){
22
setwd(outfileLoc)
33
# Calculate number of positions with the same counts
4-
script='quantile_perl_table_tagcount.pl'
4+
script <- 'quantile_perl_table_tagcount.pl'
55
Fn.Path <- system.file( file.path("Perl",script), package="permseq")
6-
CMD<-paste("perl ",Fn.Path," ",countFile, " ",chrom.ref ," ",outfile,"_output_Dnasequantile.txt",sep="")
7-
system(paste('rm -rf ',outfile,"_output_Dnasequantile.txt",sep=''))
6+
CMD <- paste("perl ", Fn.Path, " ", countFile, " ", chrom.ref , " ", outfile, "_output_Dnasequantile.txt", sep="")
7+
system(paste('rm -rf ', outfile, "_output_Dnasequantile.txt", sep=''))
88
for(i in chrList){
9-
CMD=paste(CMD,i,sep=' ')
9+
CMD <- paste(CMD, i, sep=' ')
1010
}
1111
system(CMD, intern = TRUE )
1212
# Calculate dnaseThres and knots (using quantileFunction)
13-
DNase_tags=read.table(paste(outfileLoc,'/',outfile,'_output_Dnasequantile.txt',sep=''))
14-
out=DNase_tags[order(DNase_tags[,1],decreasing=F),]
15-
q=.quantileFunction(DNase_tags,0.999)
16-
q=c(2,out[1: max(which(out[,1]<=q)),1])
13+
DNase_tags <- read.table(paste(outfileLoc, '/', outfile, '_output_Dnasequantile.txt', sep=''))
14+
out <- DNase_tags[order(DNase_tags[, 1], decreasing=F), ]
15+
q <- .quantileFunction(DNase_tags, 0.999)
16+
q <- c(2, out[1: max(which(out[, 1] <= q)), 1])
1717

18-
cut_off=NULL
18+
cut_off <- NULL
1919
for(i in 1:length(q)){
20-
cut_off=paste(cut_off,q[i],sep=' ')
20+
cut_off <- paste(cut_off, q[i], sep=' ')
2121
}
2222

23-
Dnase_counts=c(q,.quantileFunction(DNase_tags,0.9995))
24-
dnaseThres= Dnase_counts
25-
dnaseKnots=c(.quantileFunction(DNase_tags,0.9),.quantileFunction(DNase_tags,0.99),.quantileFunction(DNase_tags,0.999))
23+
Dnase_counts <- c(q, .quantileFunction(DNase_tags, 0.9995))
24+
dnaseThres <- Dnase_counts
25+
dnaseKnots <- c(.quantileFunction(DNase_tags, 0.9), .quantileFunction(DNase_tags, 0.99), .quantileFunction(DNase_tags, 0.999))
2626
for(i in chrList){
2727
# Partition genome
28-
prioroutfile=paste(i,'_',outfile,'_positions_cluster.txt',sep='')
29-
script='prior_result.pl'
30-
Fn.Path <- system.file( file.path("Perl",script), package="permseq")
31-
CMD<-paste('perl ',Fn.Path,' ',chrom.ref,' ./ ',countFile,' ', prioroutfile,sep=' ')
32-
cmd=paste(CMD,i,cut_off,sep=' ')
28+
prioroutfile <- paste(i, '_', outfile, '_positions_cluster.txt', sep='')
29+
script <- 'prior_result.pl'
30+
Fn.Path <- system.file(file.path("Perl", script), package = "permseq")
31+
CMD <- paste('perl ', Fn.Path, ' ', chrom.ref, ' ./ ', countFile, ' ', prioroutfile, sep=' ')
32+
cmd <- paste(CMD, i, cut_off, sep=' ')
3333
system(cmd, intern = TRUE )
3434
print(i)
3535
}
3636

37-
r=list(dnaseKnots,dnaseThres)
37+
r <- list(dnaseKnots, dnaseThres)
3838
return(r)
3939
}

‎R/base_clusterPositions_3cluster.R‎

Lines changed: 18 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -1,29 +1,30 @@
1-
.clusterPositions_3cluster=function(countFile,chrList,outfileLoc="./" ,chrom.ref,outfile){
1+
.clusterPositions_3cluster = function(countFile, chrList, outfileLoc="./", chrom.ref, outfile){
22
setwd(outfileLoc)
33
# Calculate number of positions with the same counts
4-
script='quantile_perl_table_tagcount.pl'
5-
Fn.Path <- system.file( file.path("Perl",script), package="permseq")
6-
CMD<-paste("perl ",Fn.Path," ",countFile, " ",chrom.ref ," ",outfile,"_output_Dnasequantile.txt",sep="")
7-
system(paste('rm -rf ',outfile,"_output_Dnasequantile.txt",sep=''))
4+
script <- 'quantile_perl_table_tagcount.pl'
5+
Fn.Path <- system.file( file.path("Perl", script), package = "permseq")
6+
CMD <- paste("perl ", Fn.Path, " ", countFile, " ", chrom.ref, " ", outfile, "_output_Dnasequantile.txt", sep = "")
7+
system(paste('rm -rf ', outfile, "_output_Dnasequantile.txt", sep=''))
88
for(i in chrList){
9-
CMD=paste(CMD,i,sep=' ')
9+
CMD <- paste(CMD, i, sep = ' ')
1010
}
1111

1212
system(CMD, intern = TRUE )
1313
# Three clusters
14-
DNase_tags=read.table(paste(outfileLoc,'/',outfile,'_output_Dnasequantile.txt',sep=''))
15-
out=DNase_tags[order(DNase_tags[,1],decreasing=F),]
16-
dnaseKnots = c(.quantileFunction(DNase_tags, 0.9),.quantileFunction(DNase_tags,0.99))
17-
dnaseThres = dnaseKnots
18-
cut_off = NULL
19-
for (i in 1:length(dnaseThres)) cut_off = paste(cut_off, dnaseThres[i], sep = " ")
14+
DNase_tags <- read.table(paste(outfileLoc, '/', outfile, '_output_Dnasequantile.txt', sep=''))
15+
out <- DNase_tags[order(DNase_tags[, 1], decreasing=F), ]
16+
dnaseKnots <- c(.quantileFunction(DNase_tags, 0.9), .quantileFunction(DNase_tags, 0.99))
17+
dnaseThres <- dnaseKnots
18+
cut_off <- NULL
19+
for (i in 1:length(dnaseThres))
20+
cut_off <- paste(cut_off, dnaseThres[i], sep = " ")
2021
for(i in chrList){
2122
# Partition genome
22-
prioroutfile=paste(i,'_',outfile,'_positions_3cluster.txt',sep='')
23-
script='prior_result.pl'
24-
Fn.Path <- system.file( file.path("Perl",script), package="permseq")
25-
CMD<-paste('perl ',Fn.Path,' ',chrom.ref,' ./ ',countFile,' ', prioroutfile,sep=' ')
26-
cmd=paste(CMD,i,cut_off,sep=' ')
23+
prioroutfile <- paste(i, '_', outfile, '_positions_3cluster.txt', sep='')
24+
script <- 'prior_result.pl'
25+
Fn.Path <- system.file( file.path("Perl", script), package="permseq")
26+
CMD <- paste('perl ', Fn.Path, ' ', chrom.ref, ' ./ ', countFile, ' ', prioroutfile, sep=' ')
27+
cmd <- paste(CMD, i, cut_off, sep=' ')
2728
system(cmd, intern = TRUE )
2829
print(i)
2930
}

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