countReads: Extract counts for RPFs and RNAs

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Extract counts for RPFs and RNAs

Description

Calculate the reads counts for gene level or transcript level.

Usage

countReads(
  RPFs,
  RNAs,
  gtf,
  level = c("tx", "gene"),
  bestpsite = 13,
  readsLen = c(28, 29),
  anchor = "5end",
  ignore.seqlevelsStyle = FALSE,
  ...
)

Arguments

RPFs	Bam file names of RPFs.
RNAs	Bam file names of RNAseq.
gtf	GTF file name for annotation.
level	Transcript or gene level.
bestpsite	numeric(1). P site postion.
readsLen	numeric(1). reads length to keep.
anchor	5end or 3end. Default is 5end.
ignore.seqlevelsStyle	Ignore the sequence name style detection or not.
...	Parameters pass to featureCounts except isGTFAnnotationFile, GTF.attrType, and annot.ext.

Value

A list with reads counts.

Examples

path <- system.file("extdata", package="ribosomeProfilingQC")
RPFs <- dir(path, "RPF.*?.[12].bam$", full.names=TRUE)
gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
RNAs <- dir(path, "mRNA.*?.[12].bam$", full.names = TRUE)
cnts <- countReads(RPFs[1], gtf=gtf, level="gene", readsLen=29)
#cnts <- countReads(RPFs[1], RNAs[1], gtf=gtf, level="gene", readsLen=29)

jianhong/ribosomeProfilingQC documentation built on April 15, 2024, 7:10 p.m.