calculateJunctionReadCounts {proActiv} | R Documentation |
Calculate the total number of junction reads overlapping with the introns of each promoter for the input junction file
calculateJunctionReadCounts( promoterCoordinates, intronRanges, file = "", fileType = "", genome = "" )
promoterCoordinates |
A GRanges object containing promoter coordinates and reduced exon coordinates by gene |
intronRanges |
A Granges object containing the annotated unique intron ranges. These ranges will be used for counting the reads |
file |
character path for the input junction bed or bam file |
fileType |
character type of the junction bed file. Either 'tophat', 'star' or 'bam' |
genome |
character genome version |
The total number of junction reads overlapping with each promoter for the input annotated intron ranges