calculateJunctionReadCounts: Calculate the total number of junction reads overlapping with...

In GoekeLab/proActiv: Estimate Promoter Activity from RNA-Seq data

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

GoekeLab/proActiv documentation built on Jan. 30, 2022, 3:52 a.m.