coverageDepth: Extract coverage depth for gene level or transcript level

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Extract coverage depth for gene level or transcript level

Description

Calculate the coverage depth for gene level or transcript level. Coverage for RPFs will be the best P site coverage. Coverage for RNAs will be the coverage for 5'end of reads.

Usage

coverageDepth(
  RPFs,
  RNAs,
  gtf,
  level = c("tx", "gene"),
  bestpsite = 13,
  readsLen = c(28, 29),
  anchor = "5end",
  region = "cds",
  ext = 5000,
  ignore.seqlevelsStyle = FALSE,
  ...
)

Arguments

RPFs	Bam file names of RPFs.
RNAs	Bam file names of RNAseq.
gtf	GTF file name for annotation or a TxDb object.
level	Transcript or gene level.
bestpsite	P site postion.
readsLen	Reads length to keep.
anchor	5end or 3end. Default is 5end.
region	Annotation region. It could be "cds", "utr5", "utr3", "exon", "transcripts", "feature with extension".
ext	Extesion region for "feature with extension".
ignore.seqlevelsStyle	Ignore the sequence name style detection or not.
...	Parameters pass to makeTxDbFromGFF

Value

A cvgd object with coverage depth.

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")
cvgs <- coverageDepth(RPFs[1], gtf=gtf, level="gene")

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