shiftReadsByFrame: Shift reads by reading frame

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Shift reads by reading frame

Description

Shift reads P site position by reading frame. After shifting, all reading frame will be set as 0

Usage

shiftReadsByFrame(reads, txdb, ignore.seqlevelsStyle = FALSE)

Arguments

reads	Output of getPsiteCoordinates
txdb	A TxDb object.
ignore.seqlevelsStyle	Ignore the sequence name style detection or not.

Value

Reads with reading frame information

Examples

library(Rsamtools)
bamfilename <- system.file("extdata", "RPF.WT.1.bam",
                           package="ribosomeProfilingQC")
yieldSize <- 10000000
bamfile <- BamFile(bamfilename, yieldSize = yieldSize)
pc <- getPsiteCoordinates(bamfile, bestpsite=11)
pc.sub <- pc[pc$qwidth %in% c(29, 30)]
library(GenomicFeatures)
library(BSgenome.Drerio.UCSC.danRer10)
txdb <- makeTxDbFromGFF(system.file("extdata",
          "Danio_rerio.GRCz10.91.chr1.gtf.gz",
          package="ribosomeProfilingQC"),
          organism = "Danio rerio",
          chrominfo = seqinfo(Drerio)["chr1"],
          taxonomyId = 7955)
pc.sub <- shiftReadsByFrame(pc.sub, txdb)

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