codonBias: Codon usage bias

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Codon usage bias

Description

Calculate the codon usage for the reads in the identified CDSs. And then compared to the reference codon usage.

Usage

codonBias(
  RPFs,
  gtf,
  genome,
  bestpsite = 13,
  readsLen = c(28, 29),
  anchor = "5end",
  ignore.seqlevelsStyle = FALSE,
  summary = TRUE,
  removeDuplicates = TRUE,
  ...
)

Arguments

RPFs	Bam file names of RPFs.
gtf	GTF file name for annotation or a TxDb object.
genome	A BSgenome object.
bestpsite	P site postion.
readsLen	Reads length to keep.
anchor	5end or 3end. Default is 5end.
ignore.seqlevelsStyle	Ignore the sequence name style detection or not.
summary	Return the summary of codon usage bias or full list.
removeDuplicates	Remove the PCR duplicates or not. Default TRUE.
...	Parameters pass to makeTxDbFromGFF

Value

A list of data frame of codon count table if summary is TRUE. list 'reads' means the counts by raw reads. list 'reference' means the counts by sequence extracted from reference by the coordinates of mapped reads. Otherwise, return the counts (reads/reference) table for each reads.

Examples

path <- system.file("extdata", package="ribosomeProfilingQC")
RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE)
gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
library(BSgenome.Drerio.UCSC.danRer10)
cb <- codonBias(RPFs[c(1,2)], gtf=gtf, genome=Drerio)

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