#===========================================================================
#findRegionInBint Find specific region (chr,start,end) in bint.bed file
#===========================================================================
#' findRegionInBint
#'
#' @param bint.bed_datapath
#' @param chr
#' @param start
#' @param end
#' @param id
#' @param twoReg
#' @param secChr
#' @param secStart
#' @param secEnd
#' @param imported
#' @param only.chr
#'
#' @return
#' @keywords internal
#'
#' @examples
findRegionInBint<- function (bint.bed_datapath, chr, start, end, id=TRUE,
twoReg=FALSE, secChr, secStart, secEnd,
imported=FALSE, only.chr=FALSE){
#test region <- c(chr1, 2997219, 12006958)
if (imported==TRUE){
bintBegin<-bint.bed_datapath
} else {
bintBegin<-read.table (bint.bed_datapath, sep='\t')
}
bintBegin<-subset (bintBegin, bintBegin[,1]==chr)
if (only.chr==FALSE){
bintBegin<-subset (bintBegin,
as.numeric(bintBegin[,2])>=as.numeric (start) |
(as.numeric(bintBegin[,3])>=as.numeric(start) &
as.numeric(bintBegin[,2])<=as.numeric(start)) )
bintBegin<-subset (bintBegin,
as.numeric(bintBegin[,3])<=as.numeric (end) |
(as.numeric(bintBegin[,3])>=as.numeric(end) &
as.numeric(bintBegin[,2])<=as.numeric(end))
)
}
print (bintBegin)
if (twoReg==TRUE){
bintBegin1<-bintBegin
bintBegin<-read.table (bint.bed_datapath, sep='\t')
bintBegin<-subset (bintBegin, bintBegin[,1]==secChr)
if (only.chr==FALSE){
bintBegin<-subset (bintBegin,
as.numeric(bintBegin[,2])>=as.numeric (secStart) |
(as.numeric(bintBegin[,3])>=as.numeric(secStart) &
as.numeric(bintBegin[,2])<=as.numeric(secStart)) )
bintBegin<-subset (bintBegin,
as.numeric(bintBegin[,3])<=as.numeric (secEnd) |
(as.numeric(bintBegin[,3])>=as.numeric(secEnd) &
as.numeric(bintBegin[,2])<=as.numeric(secEnd))
)
}
bintBegin2<-bintBegin
print (bintBegin2)
namesA<- rownames (bintBegin1)
print (namesA)
print ('names1.....maked')
namesB<- rownames (bintBegin2)
print (namesB)
print ('names2.....maked')
namesTot<- c (namesA,namesB)
print (namesTot)
bintBegin<-merge(bintBegin1, bintBegin2, by = "V1", all = TRUE)
rownames(bintBegin)<-namesTot
}
return (if (id==FALSE){bintBegin}
else {rownames(bintBegin)}
)
}
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