assignReadingFrame: Assign reading frame

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Assign reading frame

Description

Set reading frame for each reads in CDS region to frame0, frame1 and frame2.

Usage

assignReadingFrame(reads, CDS, txdb, ignore.seqlevelsStyle = FALSE)

Arguments

reads	Output of getPsiteCoordinates
CDS	Output of prepareCDS
txdb	A TxDb object. If it is set, assign reading frame for all reads. Default missing, only assign rading frame for reads in CDS.
ignore.seqlevelsStyle	Ignore the sequence name style detection or not.

Value

An GRanges object of 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=13)
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)
#CDS <- prepareCDS(txdb)
CDS <- readRDS(system.file("extdata", "CDS.rds",
                           package="ribosomeProfilingQC"))
pc.sub <- assignReadingFrame(pc.sub, CDS)

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