#' extractContact
#'
#' @param interactionSetObj
#' @param intChrFirst
#' @param intChrSecond
#'
#' @return
#' @keywords internal
#'
#' @examples
extractContact <- function (interactionSetObj, intChrFirst, intChrSecond){
##intChr= chormosome name or 'none' or 'all'
#contMa= as.data.frame(interactions(interactionSetObj)[(seqnames(anchors(interactionSetObj,type='first'))==intChrFirst&seqnames(anchors(interactionSetObj,type='second'))==intChrSecond)|(seqnames(anchors(interactionSetObj,type='first'))==intChrSecond&seqnames(anchors(interactionSetObj,type='second'))==intChrFirst)])
if (intChrFirst=='all'){
if (intChrSecond=='all'){ #allVsAll
contMa= as.data.frame(InteractionSet::interactions(interactionSetObj))
} else { #allVsChr
contMa= as.data.frame(
InteractionSet::interactions(interactionSetObj)[(
GenomicRanges::seqnames(
InteractionSet::anchors(
interactionSetObj,type='second'))==intChrSecond)])
}
} else {
if (intChrSecond=='all'){#chrVsAll
contMa= as.data.frame(
InteractionSet::interactions(interactionSetObj)[(
GenomicRanges::seqnames(
InteractionSet::anchors(
interactionSetObj,type='first'))==intChrFirst)])
} else { #chrVsChr
contMa= as.data.frame(
InteractionSet::interactions(interactionSetObj)[(
GenomicRanges::seqnames(
InteractionSet::anchors(interactionSetObj,
type='first'))==
intChrFirst&
GenomicRanges::seqnames(
InteractionSet::anchors(interactionSetObj,
type='second'))==
intChrSecond)|
(GenomicRanges::seqnames(
InteractionSet::anchors(interactionSetObj,
type='first'))==
intChrSecond &
GenomicRanges::seqnames(
InteractionSet::anchors(interactionSetObj,
type='second'))==
intChrFirst)])
}
}
#View(contMa)
#contMa= as.data.frame(interactions(interactionSetObj)[(seqnames(anchors(interactionSetObj,type='first'))==intChrFirst&seqnames(anchors(interactionSetObj,type='second'))==intChrSecond)])
collen<- length(contMa[1,])
#print (paste0('collen',collen))
collenFinal<- 8
overlen<- (collen-collenFinal)/2
#paste0('overlen:',overlen)
contMa2=matrix (ncol=8, nrow=length(contMa[,1]))
contMa2[,1]<-as.character(contMa[,1])
contMa2[,2]<-contMa[,2]
contMa2[,3]<-contMa[,3]
contMa2[,4]<-contMa[,4]
contMa2[,5]<-as.character(contMa[,5+overlen])
contMa2[,6]<-contMa[,6+overlen]
contMa2[,7]<-contMa[,7+overlen]
contMa2[,8]<-contMa[,8+overlen]
# for (i in 1:overlen/2){
# contMa=contMa[,-5]
# contMa=contMa[,-9]
# }
# contMa=contMa[,-5]
# contMa=contMa[,-5]
# contMa=contMa[,-9]
# contMa=contMa[,-9]
View (contMa)
colnames(contMa2)<- c('T_Chr','T_start','T_end','T_width','A_Chr',
'A_start','A_end','A_width')
return (contMa2)
}
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