getPsiteCoordinates {ribosomeProfilingQC} | R Documentation

## Get P site coordinates

### Description

Extract P site coordinates from a bam file to a GRanges object.

### Usage

    getPsiteCoordinates(bamfile, bestpsite, anchor = "5end")

### Arguments

`bamfile` | A BamFile object.
`bestpsite` | P site postion. See estimatePsite
`anchor` | 5end or 3end. Default is 5end.

### Value

A GRanges object with qwidth metadata which indicates the width of reads.

### Examples

    library(Rsamtools)
    bamfilename <- system.file("extdata", "RPF.WT.1.bam",
                               package="ribosomeProfilingQC")
    yieldSize <- 10000000
    bamfile <- BamFile(bamfilename, yieldSize = yieldSize)
    pc <- getPsiteCoordinates(bamfile, bestpsite=13)

[Package ribosomeProfilingQC version 1.2.1 Index]