calculatePromoterReadCounts: Calculate the promoter read counts using junction read counts...
In dnzdmrcgl/proActivTest: Estimate Promoter Activity from RNA-Seq data

Description Usage Arguments Value Examples

Calculate the promoter read counts using junction read counts approach for all the input junction files

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calculatePromoterReadCounts(exonRanges, intronRanges,
  junctionFilePaths = NULL, junctionFileLabels = NULL,
  junctionType = "tophat", numberOfCores = 1)

`exonRanges`	A GRanges object containing reduced exon ranges by gene
`intronRanges`	A Granges object containing the annotated unique intron ranges. These ranges willbe used for counting the reads
`junctionFilePaths`	A character vector. The list of junction files for which the junction read counts will be calculated
`junctionFileLabels`	A character vector. The labels of junction files for which the junction read counts will be calculated. These labels will be used as column names for the output data.frame object
`junctionType`	A character. Type of the junction bed file, either 'tophat'(default) or 'star'
`numberOfCores`	A numeric value. The number of cores to be used for counting junction reads. Defaults to 1 (no parallelization). This parameter will be used argument to mclapply function hence require 'parallel' package to be installed

A data.frame object. The number of junction reads per promoter (rows) for each sample (cols)

## Not run: 
junctionFilePaths <- c('./sample1-tophat.bed', './sample2-tophat.bed')
junctionFileLabels <- c('sample1', 'sample2')
promoterReadCounts <- calculatePromoterReadCounts(exonReducedRanges,
                                                   intronRanges.annotated,
                                                   junctionFilePaths,
                                                   junctionFileLabels,
                                                   junctionType = 'tophat',
                                                   numberOfCores = 1)

## End(Not run)