getPsiteCoordinates: Get P site coordinates

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Get P site coordinates

Description

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

Usage

getPsiteCoordinates(
  bamfile,
  bestpsite,
  anchor = "5end",
  param = ScanBamParam(what = c("qwidth"), tag = character(0), flag =
    scanBamFlag(isSecondaryAlignment = FALSE, isUnmappedQuery = FALSE,
    isNotPassingQualityControls = FALSE, isSupplementaryAlignment = FALSE))
)

Arguments

bamfile	A BamFile object.
bestpsite	P site postion. See estimatePsite
anchor	5end or 3end. Default is 5end.
param	A ScanBamParam object. Please note the 'qwidth' is required.

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)

jianhong/ribosomeProfilingQC documentation built on April 15, 2024, 7:10 p.m.