CollectRnaSeqMetrics: CollectRnaSeqMetrics

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

CollectRnaSeqMetrics

Description

Produces a summary of RNA-seq metrics from a SAM or BAM file with picard.

Usage

  CollectRnaSeqMetrics(inBams, gtfFn, featAnnoFn,
                       strandMode = c("both", "sense", "antisense"),
                       metricLevel = c("ALL_READS", "SAMPLE", "LIBRARY", "READ_GROUP"),
                       mc.cores = ezThreads())

Arguments

inBams	character(n): the filepaths of input bam files.
gtfFn	character(1): the filepath of gtf file.
featAnnoFn	character(1): the filepath of feature annotation file.
strandMode	character(1): “both”, “sense” or “antisense”.
metricLevel	character(1): the level of summarisation.
mc.cores	integer(1): the threads to use.

Value

A data.frame of metrics.

Author(s)

Ge Tan

References

http://broadinstitute.github.io/picard/picard-metric-definitions.html#RnaSeqMetrics

See Also

CollectAlignmentSummaryMetrics

Examples

  ## Not run: 
    inBam <- "/srv/gstore/projects/p2497/SCCountsApp_24762_2018-02-20--21-32-42/20171222.A-SiCSeq_SCs_P5.bam"
    gtfFn <- "/srv/GT/reference/Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_89-2017-05-31/Genes/genes.gtf"
    featAnnoFn <- "/srv/GT/reference/Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_89-2017-05-31/Genes/genes_annotation_byTranscript.txt"
    metricLevel <- "SAMPLE"
    CollectRnaSeqMetrics(inBam, gtfFn, featAnnoFn, strandMode="both", 
                         metricLevel)
  
## End(Not run)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.