frameCounts: Extract counts for gene level or transcript level

In ribosomeProfilingQC: Ribosome Profiling Quality Control

Description

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.

Usage

frameCounts(
  reads,
  level = c("tx", "gene"),
  frame0only = TRUE,
  coverageRate = FALSE
)

Arguments

reads	Output of assignReadingFrame.
level	Transcript or gene level
frame0only	Only count for reading frame 0 or not
coverageRate	Calculate for coverage or not

Value

A numeric vector with reads counts.

Examples

pcs <- readRDS(system.file("extdata", "samplePc.rds",
               package="ribosomeProfilingQC"))
cnts <- frameCounts(pcs)
cnts.gene <- frameCounts(pcs, level="gene")
cvg <- frameCounts(pcs, coverageRate=TRUE)

ribosomeProfilingQC documentation built on March 13, 2021, 2:01 a.m.