Associates the read counts on codons with the codon type for each ORF.

Description

Associates the read counts on codons with the codon type for each ORF.

Usage

codonInfo(listReadsCodon, genomeSeq, orfCoord, motifSize)

Arguments

Value

a list of 2 data.frame objects: one with the number of times each codon type is found in each ORF and one with the number of reads for each codon type in each ORF.

Examples

#for each codon in each ORF get the read coverage
#parameter listReadsCodon can be returned by the riboSeqFromBam function
#it corresponts to the 2nd element in the list returned by riboSeqFromBam
data(codonIndexCovCtrl)
listReadsCodon <- codonIndexCovCtrl

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene

#get the names of the ORFs
#grouped by transcript
cds <- GenomicFeatures::cdsBy(txdb, use.names=TRUE)
orfCoord <- cds[names(cds) %in% names(listReadsCodon)]

#get the genome, please check that the genome has the same seqlevels
genomeSeq <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
#if not rename it
#gSeq <- GenomeInfoDb::renameSeqlevels(genomeSeq,
#sub("chr", "", GenomeInfoDb::seqlevels(genomeSeq)))

#codon frequency, coverage, and annotation
codonData <- codonInfo(listReadsCodon, genomeSeq, orfCoord)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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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/codonInfo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: codonInfo
> ### Title: Associates the read counts on codons with the codon type for
> ###   each ORF.
> ### Aliases: codonInfo
> 
> ### ** Examples
> 
> #for each codon in each ORF get the read coverage
> #parameter listReadsCodon can be returned by the riboSeqFromBam function
> #it corresponts to the 2nd element in the list returned by riboSeqFromBam
> data(codonIndexCovCtrl)
> listReadsCodon <- codonIndexCovCtrl
> 
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
> 
> #get the names of the ORFs
> #grouped by transcript
> cds <- GenomicFeatures::cdsBy(txdb, use.names=TRUE)
> orfCoord <- cds[names(cds) %in% names(listReadsCodon)]
> 
> #get the genome, please check that the genome has the same seqlevels
> genomeSeq <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
> #if not rename it
> #gSeq <- GenomeInfoDb::renameSeqlevels(genomeSeq,
> #sub("chr", "", GenomeInfoDb::seqlevels(genomeSeq)))
> 
> #codon frequency, coverage, and annotation
> codonData <- codonInfo(listReadsCodon, genomeSeq, orfCoord)
Loading required package: DBI
Loading required package: tcltk
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
  call: fun(libname, pkgname)
  error: Tcl/Tk support is not available on this system
In addition: Warning messages:
1: In codonInfo(listReadsCodon, genomeSeq, orfCoord) :
  Param motifSize should be an integer! Accepted values 3, 6 or 9. Default value is 3.

2: S3 methods 'as.character.tclObj', 'as.character.tclVar', 'as.double.tclObj', 'as.integer.tclObj', 'as.logical.tclObj', 'as.raw.tclObj', 'print.tclObj', '[[.tclArray', '[[<-.tclArray', '$.tclArray', '$<-.tclArray', 'names.tclArray', 'names<-.tclArray', 'length.tclArray', 'length<-.tclArray', 'tclObj.tclVar', 'tclObj<-.tclVar', 'tclvalue.default', 'tclvalue.tclObj', 'tclvalue.tclVar', 'tclvalue<-.default', 'tclvalue<-.tclVar', 'close.tkProgressBar' were declared in NAMESPACE but not found 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>