ribosomeReleaseScore: Ribosome Release Score (RRS)

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Ribosome Release Score (RRS)

Description

RRS is calculated as the ratio of translational efficiency in the CDS with RPFs in the 3'UTR.

Usage

ribosomeReleaseScore(
  cdsTE,
  utr3TE,
  CDSsampleOrder,
  UTR3sampleOrder,
  pseudocount = 0,
  log2 = FALSE
)

Arguments

cdsTE, utr3TE	Translational efficiency of CDS and UTR3 region. Output of translationalEfficiency
CDSsampleOrder, UTR3sampleOrder	Sample order of cdsTE and utr3TE. The parameters are used to make sure that the order of CDS and UTR3 in TE is corresponding samples.
pseudocount	The number will be add to sum of reads count to avoid X/0.
log2	Do log2 transform or not.

Value

A vector of RRS.

Examples

## Not run: 
path <- system.file("extdata", package="ribosomeProfilingQC")
RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE)
RNAs <- dir(path, "mRNA.*?\\.[12].bam$", full.names=TRUE)
gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
cvgs <- coverageDepth(RPFs, RNAs, gtf)
cvgs.utr3 <- coverageDepth(RPFs, RNAs, gtf, region="utr3")
TE90 <- translationalEfficiency(cvgs, window = 90)
TE90.utr3 <- translationalEfficiency(cvgs.utr3, window = 90)
rrs <- ribosomeReleaseScore(TE90, TE90.utr3)

## End(Not run)

jianhong/ribosomeProfilingQC documentation built on April 15, 2024, 7:10 p.m.