assignReadingFrame {ribosomeProfilingQC}R Documentation

Assign reading frame

Description

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

Usage

assignReadingFrame(reads, CDS, txdb)

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.

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)

[Package ribosomeProfilingQC version 1.4.0 Index]