Relative position of the start and stop codon along the transcript

Description

Relative position of the start and stop codon along the transcript

Usage

orfRelativePos(cdsTransc, exonGRanges)

Arguments

Value

a list. A list of relative positions of the start and end of ORFs.

Examples

#make a txdb object containing the annotations for the specified species.
#In this case hg19.
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene

#get all CDSs by transcript
cds <- GenomicFeatures::cdsBy(txdb, by="tx", use.names=TRUE)

#get all exons by transcript
exonGRanges <- GenomicFeatures::exonsBy(txdb, by="tx", use.names=TRUE)

#retrieve the positions of start and end codons relative to the transcript
cdsPosTransc <- orfRelativePos(cds, exonGRanges)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(RiboProfiling)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Warning messages:
1: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'RiboProfiling' 
2: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RiboProfiling/orfRelativePos.Rd_%03d_medium.png", width=480, height=480)
> ### Name: orfRelativePos
> ### Title: Relative position of the start and stop codon along the
> ###   transcript
> ### Aliases: orfRelativePos
> 
> ### ** Examples
> 
> #make a txdb object containing the annotations for the specified species.
> #In this case hg19.
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
> 
> #get all CDSs by transcript
> cds <- GenomicFeatures::cdsBy(txdb, by="tx", use.names=TRUE)
> 
> #get all exons by transcript
> exonGRanges <- GenomicFeatures::exonsBy(txdb, by="tx", use.names=TRUE)
> 
> #retrieve the positions of start and end codons relative to the transcript
> cdsPosTransc <- orfRelativePos(cds, exonGRanges)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>