Nothing
R/Export.R
In r3Cseq: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
# TODO: The following functions are implemented for exporting the output of 3C-seq results.
# Author: Supat Thongjuea
# Contact : supat.thongjuea@imm.ox.ac.uk or supat.thongjuea@gmail.com
###############################################################################
setGeneric(
name="export3CseqRawReads2bedGraph",
def=function(object){
standardGeneric("export3CseqRawReads2bedGraph")
}
)
setMethod("export3CseqRawReads2bedGraph",
signature(object = "r3Cseq"),
function (object){
if(!is(object,"r3Cseq")){
stop("Need the r3Cseq object")
}
if(isControlInvolved(object)==FALSE){
expRawReads.GRanges<-expRawData(object)
expLabeled<-expLabel(object)
orgName <- organismName(object)
if(base::length(expRawReads.GRanges)>0){
print("making coverage vector......")
exp.read.cov <- RleList()
#***Fix the error in this version by changing from RangeData to GRanges
exp.read.cov <- coverage(expRawReads.GRanges)
export.iranges<-as(exp.read.cov,"GRanges")
export.ucsc<-as(export.iranges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=expLabeled,description="Raw reads")
file_name<-paste(expLabeled,".bedGraph",".gz",sep="")
export(export.ucsc,file_name)
print(paste("File",file_name,"' is created."))
}else{
stop("No raw reads found in the object, please run getRawReads function!!!.")
}
}
if(isControlInvolved(object)==TRUE){
expRawReads.GRanges<-expRawData(object)
contrRawReads.GRanges<-contrRawData(object)
expLabeled<-expLabel(object)
contrLabeled<-contrLabel(object)
orgName <- organismName(object)
if(base::length(expRawReads.GRanges)>0){
print("making coverage vector......")
exp.read.cov <- RleList()
contr.read.cov <- RleList()
exp.read.cov <- coverage(expRawReads.GRanges)
contr.read.cov <- coverage(contrRawReads.GRanges)
#***Fix the error in this version by changing from RangeData to GRanges
export.iranges<-as(exp.read.cov,"GRanges")
export.ucsc<-as(export.iranges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=expLabeled,description="Raw reads")
file_name<-paste(expLabeled,".bedGraph",".gz",sep="")
export(export.ucsc,file_name)
print(paste("File",file_name,"' is created."))
#***Fix the error in this version by changing from RangeData to GRanges
export.iranges<-as(contr.read.cov,"GRanges")
export.ucsc<-as(export.iranges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=contrLabeled,description="Raw reads")
file_name<-paste(contrLabeled,".bedGraph",".gz",sep="")
export(export.ucsc,file_name)
print(paste("File",file_name,"' is created."))
}else{
stop("No raw reads found in the object, please run getRawReads function!!!.")
}
}
}
)
setGeneric(
name="export3Cseq2bedGraph",
def=function(object,datatype = c("rpm", "read_count")){
standardGeneric("export3Cseq2bedGraph")
}
)
setMethod("export3Cseq2bedGraph",
signature(object = "r3Cseq"),
function (object,datatype){
if(!is(object,"r3Cseq")){
stop("Need the r3Cseq object")
}
datatype <- match.arg(datatype)
if(datatype==""){
datatype<-"rpm"
}
if(isControlInvolved(object)==FALSE){
expRPMs <-expRPM(object)
expLabeled<-expLabel(object)
if(datatype=="rpm"){
if(base::length(expRPMs)>0){
##Fix export.f by adding "as.character"
export.f <-data.frame(seqnames=as.character(seqnames(expRPMs)),start=start(expRPMs),end=end(expRPMs),score=expRPMs$RPMs)
export.GRanges<-GRanges(seqnames=export.f$seqnames,IRanges(start=export.f$start,end=export.f$end),score=export.f$score)
#export.iranges<-export.iranges[export.iranges$score>0,]<--fix the error in this version
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(expLabeled,"_RPMs",sep=""),description="read per million")
file_name<-paste(expLabeled,".RPMs.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
}else{
stop("No RPM found in the r3Cseq object, you have to run the function 'getReadCountPerRestrictionFragment' following by the function 'calculateRPM'.")
}
}else if(datatype=="read_count"){
if(base::length(expRPMs)>0){
export.f <-data.frame(seqnames=as.character(seqnames(expRPMs)),start=start(expRPMs),end=end(expRPMs),score=expRPMs$nReads)
export.GRanges<-GRanges(seqnames=export.f$seqnames,IRanges(start=export.f$start,end=export.f$end),score=export.f$score)
#export.iranges<-export.iranges[export.iranges$score>0,]
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(expLabeled,"_ReadCounts",sep=""),description="read count")
file_name<-paste(expLabeled,".ReadCounts.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
}else{
stop("No read found in the r3Cseq object, you have to run the function 'getReadCountPerRestrictionFragment' following by the function 'calculateRPM'.")
}
}else{
stop("Choose the input datatype parameter: 'read_count' or 'rpm' (reads per million)")
}
}
if(isControlInvolved(object)==TRUE){
expRPMs <-expRPM(object)
contrRPMs <-contrRPM(object)
expLabeled<-expLabel(object)
controlLabeled<-contrLabel(object)
if(datatype=="rpm"){
if(base::length(expRPMs)>0){
export.GRanges<-GRanges(seqnames =as.character(seqnames(expRPMs)),IRanges(start=start(expRPMs),end=end(expRPMs)),score=expRPMs$RPMs)
#export.iranges<-export.iranges[export.iranges$score>0,]
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(expLabeled,"_RPMs",sep=""),description="reads per million")
file_name<-paste(expLabeled,".RPMs.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
export.GRanges<-GRanges(seqnames=as.character(seqnames(contrRPMs)),IRanges(start=start(contrRPMs),end=end(contrRPMs)),score=contrRPMs$RPMs)
#export.iranges<-export.iranges[export.iranges$score>0,]
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(controlLabeled,"_RPMs",sep=""),description="reads per million")
file_name<-paste(controlLabeled,".RPMs.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
}else{
stop("No RPM found in the r3Cseq object, you have to run the function 'getReadCountPerRestrictionFragment' following by the function 'calculateRPM'.")
}
}else if(datatype=="read_count"){
if(base::length(expRPMs)>0){
export.GRanges<-GRanges(seqnames=as.character(seqnames(expRPMs)),IRanges(start=start(expRPMs),end=end(expRPMs)),score=expRPMs$nReads)
#export.iranges<-export.iranges[export.iranges$score>0,]
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(expLabeled,"_ReadCounts",sep=""),description="read count")
file_name<-paste(expLabeled,".ReadCounts.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
export.GRanges<-GRanges(seqnames=as.character(seqnames(contrRPMs)),IRanges(start=start(contrRPMs),end=end(contrRPMs)),score=contrRPMs$nReads)
#export.iranges<-export.iranges[export.iranges$score>0,]
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(controlLabeled,"_ReadCounts",sep=""),description="read count")
file_name<-paste(controlLabeled,".ReadCounts.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
}else{
stop("No RPM found in the r3Cseq object, you have to run the function 'getReadCountPerRestrictionFragment' following by the function 'calculateRPM'.")
}
}else{
stop("Choose the input datatype parameter: 'read_count' or 'rpm' (reads per million)")
}
}
}
)
setGeneric(
name="exportInteractions2text",
def=function(object){
standardGeneric("exportInteractions2text")
}
)
setMethod("exportInteractions2text",
signature(object = "r3Cseq"),
function (object){
if(!is(object,"r3Cseq")){
stop("Need the r3Cseq object")
}
if(isControlInvolved(object)==FALSE){
expInteractions<-expInteractionRegions(object)
expLabeled<-expLabel(object)
if(base::length(expInteractions)>0){
file_name<-paste(expLabeled,".interaction.txt",sep="")
export.data<-data.frame(chromosome=seqnames(expInteractions),
start=start(expInteractions),end=end(expInteractions),
nReads=expInteractions$nReads,RPMs=expInteractions$RPMs,
p.value=expInteractions$p.value,q.value=expInteractions$q.value)
export.data<-export.data[order(export.data[,7]),]
export.data$p.value<-format(export.data$p.value,scientific=T)
export.data$q.value<-format(export.data$q.value,scientific=T)
write.table(export.data,file=file_name,append=FALSE, sep="\t", quote=FALSE,row.names=FALSE, col.names=TRUE)
print(paste("File",file_name,"' is created."))
}else{
stop("No interaction regions found in the r3Cseq object, you have to run the r3Cseq pipeline.")
}
}
if(isControlInvolved(object)==TRUE){
expInteractions <-expInteractionRegions(object)
contrInteractions <- contrInteractionRegions(object)
expLabeled<-expLabel(object)
controlLabeled<-contrLabel(object)
if(base::length(expInteractions)>0){
file_name<-paste(expLabeled,".interaction.txt",sep="")
export.data<-data.frame(chromosome=seqnames(expInteractions),
start=start(expInteractions),end=end(expInteractions),
nReads=expInteractions$nReads,RPMs=expInteractions$RPMs,
p.value=expInteractions$p.value,q.value=expInteractions$q.value)
export.data<-export.data[order(export.data[,7]),]
export.data$p.value<-format(export.data$p.value,scientific=T)
export.data$q.value<-format(export.data$q.value,scientific=T)
write.table(export.data,file=file_name,append=FALSE, sep="\t", quote=FALSE,row.names=FALSE, col.names=TRUE)
print(paste("File",file_name,"' is created."))
}else{
stop("No interaction regions found in the r3Cseq object, you have to run the r3Cseq pipeline.")
}
if(base::length(contrInteractions)>0){
file_name<-paste(controlLabeled,".interaction.txt",sep="")
export.data<-data.frame(chromosome=seqnames(contrInteractions),
start=start(contrInteractions),end=end(contrInteractions),
nReads=contrInteractions$nReads,RPMs=contrInteractions$RPMs,
p.value=contrInteractions$p.value,q.value=contrInteractions$q.value)
export.data<-export.data[order(export.data[,7]),]
export.data$p.value<-format(export.data$p.value,scientific=T)
export.data$q.value<-format(export.data$q.value,scientific=T)
write.table(export.data,file=file_name,append=FALSE, sep="\t", quote=FALSE,row.names=FALSE, col.names=TRUE)
print(paste("File",file_name,"' is created."))
}else{
stop("No interaction regions found in the r3Cseq object, you have to run the r3Cseq pipeline.")
}
}
}
)
setGeneric(
name="exportBatchInteractions2text",
def=function(object){
standardGeneric("exportBatchInteractions2text")
}
)
setMethod("exportBatchInteractions2text",
signature(object = "r3CseqInBatch"),
function (object){
if(!is(object,"r3CseqInBatch")){
stop("Need the r3CseqInBatch object")
}
if(isControlInvolved(object)==TRUE){
expInteractions <-expInteractionRegions(object)
contrInteractions <- contrInteractionRegions(object)
if(base::length(expInteractions)>0){
file_name<-"Batch.experiment.interaction.txt"
export.data<-data.frame(chromosome=seqnames(expInteractions),
start=start(expInteractions),end=end(expInteractions),
nReads=expInteractions$nReads,RPMs=expInteractions$RPMs,
p.value=expInteractions$p.value,q.value=expInteractions$q.value)
export.data<-export.data[order(export.data[,7]),]
export.data$p.value<-format(export.data$p.value,scientific=T)
export.data$q.value<-format(export.data$q.value,scientific=T)
write.table(export.data,file=file_name,append=FALSE, sep="\t", quote=FALSE,row.names=FALSE, col.names=TRUE)
print(paste("File",file_name,"' is created."))
}else{
stop("No interaction regions found in the r3Cseq object, you have to run the r3Cseq pipeline.")
}
if(base::length(contrInteractions)>0){
file_name<-"Batch.control.interaction.txt"
export.data<-data.frame(chromosome=seqnames(contrInteractions),
start=start(contrInteractions),end=end(contrInteractions),
nReads=contrInteractions$nReads,RPMs=contrInteractions$RPMs,
p.value=contrInteractions$p.value,q.value=contrInteractions$q.value)
export.data<-export.data[order(export.data[,7]),]
export.data$p.value<-format(export.data$p.value,scientific=T)
export.data$q.value<-format(export.data$q.value,scientific=T)
write.table(export.data,file=file_name,append=FALSE, sep="\t", quote=FALSE,row.names=FALSE, col.names=TRUE)
print(paste("File",file_name,"' is created."))
}else{
stop("No interaction regions found in the r3Cseq object, you have to run the r3Cseq pipeline.")
}
}
}
)
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# TODO: The following functions are implemented for exporting the output of 3C-seq results.
# Author: Supat Thongjuea
# Contact : supat.thongjuea@imm.ox.ac.uk or supat.thongjuea@gmail.com
###############################################################################
setGeneric(
name="export3CseqRawReads2bedGraph",
def=function(object){
standardGeneric("export3CseqRawReads2bedGraph")
}
)
setMethod("export3CseqRawReads2bedGraph",
signature(object = "r3Cseq"),
function (object){
if(!is(object,"r3Cseq")){
stop("Need the r3Cseq object")
}
if(isControlInvolved(object)==FALSE){
expRawReads.GRanges<-expRawData(object)
expLabeled<-expLabel(object)
orgName <- organismName(object)
if(base::length(expRawReads.GRanges)>0){
print("making coverage vector......")
exp.read.cov <- RleList()
#***Fix the error in this version by changing from RangeData to GRanges
exp.read.cov <- coverage(expRawReads.GRanges)
export.iranges<-as(exp.read.cov,"GRanges")
export.ucsc<-as(export.iranges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=expLabeled,description="Raw reads")
file_name<-paste(expLabeled,".bedGraph",".gz",sep="")
export(export.ucsc,file_name)
print(paste("File",file_name,"' is created."))
}else{
stop("No raw reads found in the object, please run getRawReads function!!!.")
}
}
if(isControlInvolved(object)==TRUE){
expRawReads.GRanges<-expRawData(object)
contrRawReads.GRanges<-contrRawData(object)
expLabeled<-expLabel(object)
contrLabeled<-contrLabel(object)
orgName <- organismName(object)
if(base::length(expRawReads.GRanges)>0){
print("making coverage vector......")
exp.read.cov <- RleList()
contr.read.cov <- RleList()
exp.read.cov <- coverage(expRawReads.GRanges)
contr.read.cov <- coverage(contrRawReads.GRanges)
#***Fix the error in this version by changing from RangeData to GRanges
export.iranges<-as(exp.read.cov,"GRanges")
export.ucsc<-as(export.iranges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=expLabeled,description="Raw reads")
file_name<-paste(expLabeled,".bedGraph",".gz",sep="")
export(export.ucsc,file_name)
print(paste("File",file_name,"' is created."))
#***Fix the error in this version by changing from RangeData to GRanges
export.iranges<-as(contr.read.cov,"GRanges")
export.ucsc<-as(export.iranges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=contrLabeled,description="Raw reads")
file_name<-paste(contrLabeled,".bedGraph",".gz",sep="")
export(export.ucsc,file_name)
print(paste("File",file_name,"' is created."))
}else{
stop("No raw reads found in the object, please run getRawReads function!!!.")
}
}
}
)
setGeneric(
name="export3Cseq2bedGraph",
def=function(object,datatype = c("rpm", "read_count")){
standardGeneric("export3Cseq2bedGraph")
}
)
setMethod("export3Cseq2bedGraph",
signature(object = "r3Cseq"),
function (object,datatype){
if(!is(object,"r3Cseq")){
stop("Need the r3Cseq object")
}
datatype <- match.arg(datatype)
if(datatype==""){
datatype<-"rpm"
}
if(isControlInvolved(object)==FALSE){
expRPMs <-expRPM(object)
expLabeled<-expLabel(object)
if(datatype=="rpm"){
if(base::length(expRPMs)>0){
##Fix export.f by adding "as.character"
export.f <-data.frame(seqnames=as.character(seqnames(expRPMs)),start=start(expRPMs),end=end(expRPMs),score=expRPMs$RPMs)
export.GRanges<-GRanges(seqnames=export.f$seqnames,IRanges(start=export.f$start,end=export.f$end),score=export.f$score)
#export.iranges<-export.iranges[export.iranges$score>0,]<--fix the error in this version
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(expLabeled,"_RPMs",sep=""),description="read per million")
file_name<-paste(expLabeled,".RPMs.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
}else{
stop("No RPM found in the r3Cseq object, you have to run the function 'getReadCountPerRestrictionFragment' following by the function 'calculateRPM'.")
}
}else if(datatype=="read_count"){
if(base::length(expRPMs)>0){
export.f <-data.frame(seqnames=as.character(seqnames(expRPMs)),start=start(expRPMs),end=end(expRPMs),score=expRPMs$nReads)
export.GRanges<-GRanges(seqnames=export.f$seqnames,IRanges(start=export.f$start,end=export.f$end),score=export.f$score)
#export.iranges<-export.iranges[export.iranges$score>0,]
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(expLabeled,"_ReadCounts",sep=""),description="read count")
file_name<-paste(expLabeled,".ReadCounts.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
}else{
stop("No read found in the r3Cseq object, you have to run the function 'getReadCountPerRestrictionFragment' following by the function 'calculateRPM'.")
}
}else{
stop("Choose the input datatype parameter: 'read_count' or 'rpm' (reads per million)")
}
}
if(isControlInvolved(object)==TRUE){
expRPMs <-expRPM(object)
contrRPMs <-contrRPM(object)
expLabeled<-expLabel(object)
controlLabeled<-contrLabel(object)
if(datatype=="rpm"){
if(base::length(expRPMs)>0){
export.GRanges<-GRanges(seqnames =as.character(seqnames(expRPMs)),IRanges(start=start(expRPMs),end=end(expRPMs)),score=expRPMs$RPMs)
#export.iranges<-export.iranges[export.iranges$score>0,]
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(expLabeled,"_RPMs",sep=""),description="reads per million")
file_name<-paste(expLabeled,".RPMs.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
export.GRanges<-GRanges(seqnames=as.character(seqnames(contrRPMs)),IRanges(start=start(contrRPMs),end=end(contrRPMs)),score=contrRPMs$RPMs)
#export.iranges<-export.iranges[export.iranges$score>0,]
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(controlLabeled,"_RPMs",sep=""),description="reads per million")
file_name<-paste(controlLabeled,".RPMs.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
}else{
stop("No RPM found in the r3Cseq object, you have to run the function 'getReadCountPerRestrictionFragment' following by the function 'calculateRPM'.")
}
}else if(datatype=="read_count"){
if(base::length(expRPMs)>0){
export.GRanges<-GRanges(seqnames=as.character(seqnames(expRPMs)),IRanges(start=start(expRPMs),end=end(expRPMs)),score=expRPMs$nReads)
#export.iranges<-export.iranges[export.iranges$score>0,]
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(expLabeled,"_ReadCounts",sep=""),description="read count")
file_name<-paste(expLabeled,".ReadCounts.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
export.GRanges<-GRanges(seqnames=as.character(seqnames(contrRPMs)),IRanges(start=start(contrRPMs),end=end(contrRPMs)),score=contrRPMs$nReads)
#export.iranges<-export.iranges[export.iranges$score>0,]
export.GRanges<-export.GRanges[export.GRanges$score>0,]
export.ucsc<-as(export.GRanges,"UCSCData")
export.ucsc@trackLine <- new("GraphTrackLine",type="bedGraph",name=paste(controlLabeled,"_ReadCounts",sep=""),description="read count")
file_name<-paste(controlLabeled,".ReadCounts.bedGraph.gz",sep="")
export(export.ucsc,file_name,"bedGraph")
print(paste("File",file_name,"' is created."))
}else{
stop("No RPM found in the r3Cseq object, you have to run the function 'getReadCountPerRestrictionFragment' following by the function 'calculateRPM'.")
}
}else{
stop("Choose the input datatype parameter: 'read_count' or 'rpm' (reads per million)")
}
}
}
)
setGeneric(
name="exportInteractions2text",
def=function(object){
standardGeneric("exportInteractions2text")
}
)
setMethod("exportInteractions2text",
signature(object = "r3Cseq"),
function (object){
if(!is(object,"r3Cseq")){
stop("Need the r3Cseq object")
}
if(isControlInvolved(object)==FALSE){
expInteractions<-expInteractionRegions(object)
expLabeled<-expLabel(object)
if(base::length(expInteractions)>0){
file_name<-paste(expLabeled,".interaction.txt",sep="")
export.data<-data.frame(chromosome=seqnames(expInteractions),
start=start(expInteractions),end=end(expInteractions),
nReads=expInteractions$nReads,RPMs=expInteractions$RPMs,
p.value=expInteractions$p.value,q.value=expInteractions$q.value)
export.data<-export.data[order(export.data[,7]),]
export.data$p.value<-format(export.data$p.value,scientific=T)
export.data$q.value<-format(export.data$q.value,scientific=T)
write.table(export.data,file=file_name,append=FALSE, sep="\t", quote=FALSE,row.names=FALSE, col.names=TRUE)
print(paste("File",file_name,"' is created."))
}else{
stop("No interaction regions found in the r3Cseq object, you have to run the r3Cseq pipeline.")
}
}
if(isControlInvolved(object)==TRUE){
expInteractions <-expInteractionRegions(object)
contrInteractions <- contrInteractionRegions(object)
expLabeled<-expLabel(object)
controlLabeled<-contrLabel(object)
if(base::length(expInteractions)>0){
file_name<-paste(expLabeled,".interaction.txt",sep="")
export.data<-data.frame(chromosome=seqnames(expInteractions),
start=start(expInteractions),end=end(expInteractions),
nReads=expInteractions$nReads,RPMs=expInteractions$RPMs,
p.value=expInteractions$p.value,q.value=expInteractions$q.value)
export.data<-export.data[order(export.data[,7]),]
export.data$p.value<-format(export.data$p.value,scientific=T)
export.data$q.value<-format(export.data$q.value,scientific=T)
write.table(export.data,file=file_name,append=FALSE, sep="\t", quote=FALSE,row.names=FALSE, col.names=TRUE)
print(paste("File",file_name,"' is created."))
}else{
stop("No interaction regions found in the r3Cseq object, you have to run the r3Cseq pipeline.")
}
if(base::length(contrInteractions)>0){
file_name<-paste(controlLabeled,".interaction.txt",sep="")
export.data<-data.frame(chromosome=seqnames(contrInteractions),
start=start(contrInteractions),end=end(contrInteractions),
nReads=contrInteractions$nReads,RPMs=contrInteractions$RPMs,
p.value=contrInteractions$p.value,q.value=contrInteractions$q.value)
export.data<-export.data[order(export.data[,7]),]
export.data$p.value<-format(export.data$p.value,scientific=T)
export.data$q.value<-format(export.data$q.value,scientific=T)
write.table(export.data,file=file_name,append=FALSE, sep="\t", quote=FALSE,row.names=FALSE, col.names=TRUE)
print(paste("File",file_name,"' is created."))
}else{
stop("No interaction regions found in the r3Cseq object, you have to run the r3Cseq pipeline.")
}
}
}
)
setGeneric(
name="exportBatchInteractions2text",
def=function(object){
standardGeneric("exportBatchInteractions2text")
}
)
setMethod("exportBatchInteractions2text",
signature(object = "r3CseqInBatch"),
function (object){
if(!is(object,"r3CseqInBatch")){
stop("Need the r3CseqInBatch object")
}
if(isControlInvolved(object)==TRUE){
expInteractions <-expInteractionRegions(object)
contrInteractions <- contrInteractionRegions(object)
if(base::length(expInteractions)>0){
file_name<-"Batch.experiment.interaction.txt"
export.data<-data.frame(chromosome=seqnames(expInteractions),
start=start(expInteractions),end=end(expInteractions),
nReads=expInteractions$nReads,RPMs=expInteractions$RPMs,
p.value=expInteractions$p.value,q.value=expInteractions$q.value)
export.data<-export.data[order(export.data[,7]),]
export.data$p.value<-format(export.data$p.value,scientific=T)
export.data$q.value<-format(export.data$q.value,scientific=T)
write.table(export.data,file=file_name,append=FALSE, sep="\t", quote=FALSE,row.names=FALSE, col.names=TRUE)
print(paste("File",file_name,"' is created."))
}else{
stop("No interaction regions found in the r3Cseq object, you have to run the r3Cseq pipeline.")
}
if(base::length(contrInteractions)>0){
file_name<-"Batch.control.interaction.txt"
export.data<-data.frame(chromosome=seqnames(contrInteractions),
start=start(contrInteractions),end=end(contrInteractions),
nReads=contrInteractions$nReads,RPMs=contrInteractions$RPMs,
p.value=contrInteractions$p.value,q.value=contrInteractions$q.value)
export.data<-export.data[order(export.data[,7]),]
export.data$p.value<-format(export.data$p.value,scientific=T)
export.data$q.value<-format(export.data$q.value,scientific=T)
write.table(export.data,file=file_name,append=FALSE, sep="\t", quote=FALSE,row.names=FALSE, col.names=TRUE)
print(paste("File",file_name,"' is created."))
}else{
stop("No interaction regions found in the r3Cseq object, you have to run the r3Cseq pipeline.")
}
}
}
)
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