coverageRates: Calculate coverage rate

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Calculate coverage rate

Description

Coverage is a measure as percentage of position with reads along the CDS. Coverage rate calculate coverage rate for RPFs and mRNAs in gene level. Coverage will be calculated based on best P sites for RPFs and 5'end for RNA-seq.

Usage

coverageRates(cvgs, RPFsampleOrder, mRNAsampleOrder)

Arguments

cvgs	Output of coverageDepth
RPFsampleOrder, mRNAsampleOrder	Sample order of RPFs and mRNAs. The parameters are used to make sure that the order of RPFs and mRNAs in cvgs is corresponding samples.

Value

A list with coverage rate.

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")
cvgs <- coverageDepth(RPFs[1], gtf=gtf, level="gene")
cr <- coverageRates(cvgs)

jianhong/ribosomeProfilingQC documentation built on Nov. 3, 2024, 6:33 p.m.