(original) (raw)

## ----knitr, echo=FALSE, results="hide"---------------------------------------- library("knitr") opts_chunk$set(tidy=FALSE,dev="png",fig.show="hide", fig.width=4,fig.height=4.5, message=FALSE) ## ----<style-knitr, 1="" eval="TRUE," echo="FALSE," results="asis" -------------------="" biocstyle::latex()="" ##="" ----options,echo="FALSE-------------------------------------------------------" options(digits="3," width="80," prompt=" " ,="" continue=" " )="" ----import_library_noecho,echo="TRUE,eval=FALSE-------------------------------" #="" library(riboprofiling)="" listinputbam="" <-="" c(="" bamfile("http:="" genomique.info="" data="" public="" riboprofiling="" ctrl.bam"),="" nutlin2h.bam")="" covdata="" riboseqfrombam(listinputbam,="" genomename="hg19" ----import_library,echo="FALSE------------------------------------------------" suppresswarnings(suppressmessages(library(riboprofiling)))="" ----riboseqfrombam,echo="FALSE,eval=TRUE,dev=c("png"),fig.width=7-------------" myfilectrl="" system.file("extdata",="" "ctrl_sample.bam",="" package="RiboProfiling" myfilenutlin2h="" "nutlin2h_sample.bam",="" listeinputbam="" c(myfilectrl,="" myfilenutlin2h)="" txdb="" txdb.hsapiens.ucsc.hg19.knowngene::txdb.hsapiens.ucsc.hg19.knowngene="" suppressmessages(="" suppresswarnings(="" riboseqfrombam(="" listeinputbam,="" listshiftvalue="c(-14," -14)="" ----galignments_from_bam,echo="TRUE,eval=FALSE--------------------------------" aln="" readgalignments(="" ctrl.bam")="" ----hist_quick,echo="TRUE,eval=TRUE,dev=c('png')------------------------------" data(ctrlgalignments)="" ctrlgalignments="" matchlendistr="" histmatchlength(aln,="" 0)="" matchlendistr[[2]]="" ----covaroundtss_quick,eval="FALSE,echo=TRUE,split=TRUE-----------------------" #transform="" the="" galignments="" object="" into="" a="" granges="" #(faster="" processing="" of="" object)="" alngranges="" readstostartorend(aln,="" what="start" #txdb="" with="" annotations="" txdb.hsapiens.ucsc.hg19.knowngene="" onebinranges="" aroundpromoter(txdb,="" alngranges,="" percbestexpressed="0.001)" #the="" coverage="" in="" tss="" flanking="" region="" for="" reads="" match="" sizes="" 29:31="" listpromotercov="" readstartcov(="" onebinranges,="" matchsize="c(29:31)," fixedinterval="c(-20," 20),="" renamechr="aroundTSS" charperc="perc" plotsummarizedcov(listpromotercov)="" ----tss_cov,echo="FALSE,eval=TRUE,fig.height=10,dev=c('png')------------------" #make="" containing="" specified="" species.="" #in="" this="" case="" hg19.="" #please="" make="" sure="" that="" seqnames="" correspond="" to="" #of="" alignment="" files="" ("chr"="" particle)="" #if="" not="" rename="" seqlevels="" #renameseqlevels(txdb,="" sub("chr",="" "",="" seqlevels(txdb)))="" #get="" around="" promoter="" 0.1%="" best="" expressed="" cdss="" summarized="" read="" suppressmessages(plotsummarizedcov(listpromotercov))="" ----countreads_echo,echo="TRUE,eval=FALSE-------------------------------------" #keep="" only="" 30-33="" alngranges[which(!is.na(match(alngranges$score,30:33)))]="" all="" by="" transcript="" cds="" cdsby(txdb,="" use.names="TRUE)" exons="" exongranges="" exonsby(txdb,="" per="" relative="" position="" start="" and="" end="" codons="" cdspostransc="" orfrelativepos(cds,="" exongranges)="" #compute="" counts="" on="" different="" features="" #after="" applying="" shift="" value="" along="" countsdatactrl1="" countshiftreads(="" shiftvalue="-14" head(countsdatactrl1[[1]])="" listcountsplots="" countsplot(="" list(countsdatactrl1[[1]]),="" grep("_counts$",="" colnames(countsdatactrl1[[1]])),="" ----countreads,echo="FALSE,eval=TRUE,fig.width=7,dev=c('png')-----------------" genomicfeatures::cdsby(txdb,="" genomicfeatures::exonsby(txdb,="" #cdspostransc="" data("cdspostransc")="" after="" exongranges[names(cdspostransc)],="" cdspostransc,="" -14="" invisible(capture.output(="" print(listcountsplots))="" head(countsdatactrl1[[1]],="" n="3)" ----codon_cov_position,echo="TRUE,eval=TRUE-----------------------------------" data(codonindexcovctrl)="" head(codonindexcovctrl[[1]],="" ----codonanalysis_echo,echo="TRUE,eval=FALSE----------------------------------" listreadscodon="" countsdatactrl1[[2]]="" names="" orfs="" grouped="" orfcoord="" cds[names(cds)="" %in%="" names(listreadscodon)]="" #chromosome="" should="" between="" bam,="" annotations,="" genome="" genomeseq="" bsgenome.hsapiens.ucsc.hg19="" #codon="" frequency,="" coverage,="" annotation="" codondata="" codoninfo(listreadscodon,="" genomeseq,="" orfcoord)="" ----codonanalysis,echo="FALSE,eval=TRUE---------------------------------------" which="" we="" have="" #grouped="" bsgenome.hsapiens.ucsc.hg19::bsgenome.hsapiens.ucsc.hg19="" ----countreads_res,results="TRUE,echo=TRUE,split=FALSE------------------------" data("codondatactrl")="" head(codondatactrl[[1]],="" ----codonpca,echo="TRUE,eval=TRUE,dev=c("png")--------------------------------" codonusage="" codondata[[1]]="" codoncovmatrix="" codondata[[2]]="" genes="" minimum="" number="" nbrreadsgene="" apply(codoncovmatrix,="" 1,="" sum)="" ixexpgenes="" which(nbrreadsgene="">= 50) codonCovMatrix <- codonCovMatrix[ixExpGenes, ] #get the PCA on the codon coverage codonCovMatrixTransp <- t(codonCovMatrix) rownames(codonCovMatrixTransp) <- colnames(codonCovMatrix) colnames(codonCovMatrixTransp) <- rownames(codonCovMatrix) listPCACodonCoverage <- codonPCA(codonCovMatrixTransp, "codonCoverage") listPCACodonCoverage[[2]] ## ----sessInfo,echo=TRUE,eval=TRUE--------------------------------------------- sessionInfo() </style-knitr,>