frameCounts {ribosomeProfilingQC} | R Documentation |
Calculate the reads counts or coverage rate for gene level or transcript level. Coverage is determined by measuring the proportion of in-frame CDS positions with >= 1 reads.
frameCounts( reads, level = c("tx", "gene"), frame0only = TRUE, coverageRate = FALSE )
reads |
Output of assignReadingFrame. |
level |
Transcript or gene level |
frame0only |
Only count for reading frame 0 or not |
coverageRate |
Calculate for coverage or not |
A numeric vector with reads counts.
pcs <- readRDS(system.file("extdata", "samplePc.rds", package="ribosomeProfilingQC")) cnts <- frameCounts(pcs) cnts.gene <- frameCounts(pcs, level="gene") cvg <- frameCounts(pcs, coverageRate=TRUE)