calculateJunctionReadCounts: Calculate the total number of junction reads overlapping with...
In dnzdmrcgl/proActivTest: Estimate Promoter Activity from RNA-Seq data

Description Usage Arguments Value Examples

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

1 2	calculateJunctionReadCounts(exonRanges, intronRanges, junctionFilePath = "", junctionType = "tophat")

`exonRanges`	A GRanges object containing reduced exon ranges by gene
`intronRanges`	A Granges object containing the annotated unique intron ranges. These ranges will be used for counting the reads
`junctionFilePath`	character path for the input junction bed file
`junctionType`	character type of the junction bed file. Either 'tophat' or 'star'

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

## Not run: 
junctionFilePath <- './sample1-tophat.bed'
junctionCounts <- calculateJunctionReadCounts(exonReducedRanges,
                                               intronRanges.annotated,
                                               junctionFilePath,
                                               junctionType = 'tophat')
## End(Not run)