analyzeDuprates: Read in a BAM file and count the tags falling on the features...

In imbforge/dupRadar: Assessment of duplication rates in RNA-Seq datasets

Read in a BAM file and count the tags falling on the features described in the GTF file

Description

analyzeDuprates returns a data.frame with tag counts

Usage

analyzeDuprates(
  bam,
  gtf,
  stranded = 0,
  paired = FALSE,
  threads = 1,
  verbose = FALSE,
  ...
)

Arguments

bam	The bam file containing the duplicate-marked reads
gtf	The gtf file describing the features
stranded	Whether the reads are strand specific
paired	Paired end experiment?
threads	The number of threads to be used for counting
verbose	Whether to output Rsubread messages into the console
...	Other params sent to featureCounts

Details

This function makes use of the Rsubread package to count tags on the GTF features in different scenarios. The scenarios are the 4 possible combinations of allowing multimappers (yes/no) and duplicate reads (yes/no).

Value

A data.frame with counts on features, with and without taking into account multimappers/duplicated reads

Examples

bam <- system.file("extdata",
                   "wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2_duprm.bam",
                   package="dupRadar")
gtf <- system.file("extdata","genes.gtf",package="dupRadar")
stranded <- 2    # '0' (unstranded), '1' (stranded) and '2' (reverse)
paired   <- FALSE
threads  <- 4

# call the duplicate marker and analyze the reads
dm <- analyzeDuprates(bam,gtf,stranded,paired,threads)

imbforge/dupRadar documentation built on Oct. 18, 2023, 8:54 a.m.