bgThreshold <-
function( bgFiles, cutoff, mergeDist=50, positive=TRUE, negative=FALSE){
bgnames<-basename(removeext(bgFiles))
if(positive==TRUE){
outnames<-paste0(bgnames,"_gt",abs(cutoff),".bg")
cmdString <- paste(
"awk '$4 >=",abs(cutoff),"'",bgFiles,
if( !is.null(mergeDist) ){ "| bedtools merge -c 4 -o max -i stdin -d" },
if( !is.null(mergeDist) ){ mergeDist },
">",outnames
)
for(i in 1:length(bgFiles)){
print( cmdString[i] )
system( cmdString[i] )
}
}
if(negative==TRUE){
outnames<-paste0(bgnames,"_lt",-abs(cutoff),".bg")
cmdString <- paste(
"awk '$4 <=",-abs(cutoff),"'",bgFiles,
if( !is.null(mergeDist) ){ "| bedtools merge -c 4 -o min -i stdin -d" },
if( !is.null(mergeDist) ){ mergeDist },
">",outnames
)
for(i in 1:length(bgFiles)){
print( cmdString[i] )
system( cmdString[i] )
}
}
return(outnames)
}
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