coverageDepth {ribosomeProfilingQC} | R Documentation

## 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,
      ...
    )

### 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".
`...` | 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")

[Package ribosomeProfilingQC version 1.6.1 Index]