Calculate the total number of junction reads overlapping with the introns of each promoter for the input junction file

Source: R/junction-read-count.R

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 = ""
)

Arguments

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

Value

The total number of junction reads overlapping with each promoter for the input annotated intron ranges