getDupRateFromBam: Duplication rate from Bam of RNA-Seq.

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Duplication rate from Bam of RNA-Seq.

Description

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

Usage

  getDupRateFromBam(bamFile, param = NULL, gtfFn,
                    stranded = c("both", "sense", "antisense"),
                    paired = FALSE, threads = 1)

Arguments

bamFile	character(1): filename of bamFile.
param	ezRun param list.
gtfFn	character(1): The gtf file describing the features
stranded	character(1): “both”, “sense” or “antisense”
paired	logical: Paired end experiment?
threads	Integer: The number of threads to be used for counting.

Details

It uses the implementation of package dupRadar.

Value

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

Author(s)

Ge Tan

References

Sayols S, Scherzinger D and Klein H (2016). "dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data." BMC Bioinformatics, 17, pp. 428. doi: 10.1186/s12859-016-1276-2, http://dx.doi.org/10.1186/s12859-016-1276-2.

Examples

  ## Not run: 
    bamFile <- "/srv/gstore/projects/p2438/STAR_18564_2017-06-12--13-46-30/26EV_BL_A.bam"
    gtfFn <- "/srv/GT/reference/Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_89-2017-05-31/Genes/genes.gtf"
    stranded <- "antisense"
    paired <- FALSE
    threads <- 4
    resBam <- getDupRateFromBam(bamFile=bamFile, gtfFn=gtfFn,
                                    stranded=stranded,
                                    paired=paired, threads=threads)
  
## End(Not run)

uzh/ezRun documentation built on May 4, 2024, 3:23 p.m.