| coverageRates {ribosomeProfilingQC} | R Documentation |
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.
coverageRates(cvgs, RPFsampleOrder, mRNAsampleOrder)
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. |
A list with coverage rate.
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)