#' readENCODE read broadPeak and narrowPeak formats and return a GRanges object
#'
#' @param filename filename to import
#'
#' @import GenomicRanges
#' @export
readENCODE <- function(filename){
type <- tail(strsplit(basename(filename),"[.]")[[1]],1)
pks <- NULL
pks <- try(read.delim(filename,head=F,sep="\t",stringsAsFactor=F),silent = T)
if(is(pks)=="try-error") return(NULL)
if(type=="narrowPeak"){
colnames(pks) <- c("seqnames","start","end","name","score","strand","signal","pValue",
"qValue","peak")
}else if(type=="broadPeak"){
colnames(pks) <- c("seqnames","start","end","name","score","strand","signal","pValue",
"qValue")
}else{
colnames(pks) <- c("seqnames","start","end","score")
pks$strand <- "*"
}
pks$strand <- ifelse(!(pks$strand %in% c("+","-","*")),"*",pks$strand)
as(pks,"GRanges")
}
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