frameCounts: Extract counts for gene level or transcript level

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Extract counts for gene level or transcript level

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)

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