calculatePromoterReadCounts {proActiv} | R Documentation

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

### Description

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

### Usage

    calculatePromoterReadCounts(
      promoterAnnotation,
      files = NULL,
      fileLabels = NULL,
      fileType = NULL,
      genome = NULL,
      numberOfCores = 1
    )

### Arguments

`promoterAnnotation` | A PromoterAnnotation object containing the reduced exon ranges, annotated intron ranges, promoter coordinates and the promoter id mapping
`files` | A character vector. The list of junction or BAM files for which the junction read counts will be calculated
`fileLabels` | A character vector. The labels of junction or BAM files for which the junction read counts will be calculated. These labels will be used as column names for the output data.frame object
`fileType` | A character. Type of the junction bed or bam file, either 'tophat', 'star' or 'bam
`genome` | A character. Genome version used. Must be specified if input is a BAM file. Defaults to NULL
`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 as an argument to BiocParallel::bplapply

### Value

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

[Package proActiv version 1.2.0 Index]