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 1.2.1 Index]