translationalEfficiency: Translational Efficiency

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Translational Efficiency

Description

Calculate Translational Efficiency (TE). TE is defined as the ratios of the absolute level of ribosome occupancy divided by RNA levels for transcripts.

Usage

translationalEfficiency(
  x,
  window,
  RPFsampleOrder,
  mRNAsampleOrder,
  pseudocount = 1,
  log2 = FALSE,
  normByLibSize = FALSE,
  shrink = FALSE,
  ...
)

Arguments

x	Output of getFPKM or normByRUVs. if window is set, it must be output of coverageDepth.
window	numeric(1). window size for maximal counts.
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.
pseudocount	The number will be add to sum of reads count to avoid X/0.
log2	Do log2 transform or not.
normByLibSize	Normalization by library size or not. If window size is provided and normByLibSize is set to TRUE, the coverage will be normalized by library size.
shrink	Shrink the TE or not.
...	Parameters will be passed to ash function from ashr.

Value

A list with RPFs, mRNA levels and TE as a matrix with translational efficiency

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")
cnts <- countReads(RPFs, RNAs, gtf, level="gene")
fpkm <- getFPKM(cnts)
te <- translationalEfficiency(fpkm)

## End(Not run)

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