assignReadingFrame {ribosomeProfilingQC} | R Documentation |
Set reading frame for each reads in CDS region to frame0, frame1 and frame2.
assignReadingFrame(reads, CDS, txdb)
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. |
An GRanges object of reads with reading frame information.
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)