calculateJunctionReadCounts {proActiv} | R Documentation

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

### Description

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

### Usage

    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

[Package proActiv version 1.2.0 Index]