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

analyzeDuprates returns a data.frame with tag counts

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

Value

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

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).

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)