R: Plots the summarized coverage in a specified range (e.g....
plotSummarizedCov
R Documentation
Plots the summarized coverage in a specified range (e.g. around TSS)
for the specified match sizes
Description
Plots the summarized coverage in a specified range (e.g. around TSS)
for the specified match sizes
Usage
plotSummarizedCov(covSummarized)
Arguments
covSummarized
a list of GRanges objects.
For each matchSize a GRanges object of the summarized coverage.
Value
a ggplot2 plot of read coverage in interval
Examples
#read the BAM file into a GAlignments object using
#GenomicAlignments::readGAlignments
#the GAlignments object should be similar to ctrlGAlignments
data(ctrlGAlignments)
aln <- ctrlGAlignments
#transform the GAlignments object into a GRanges object (faster processing)
alnGRanges <- readsToStartOrEnd(aln, what="start")
#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
#Please make sure that seqnames of txdb correspond to
#the seqnames of the alignment files ("chr" particle)
#if not rename the txdb seqlevels
#renameSeqlevels(txdb, sub("chr", "",seqlevels(txdb)))
#get the flanking region around the promoter of the best expressed CDSs
oneBinRanges <- aroundPromoter(txdb, alnGRanges)
#the read start coverage around the TSS as a percentage for all match sizes.
covSummarized <- readStartCov(alnGRanges, oneBinRanges, matchSize="all",
c(-20,20), "aroundTSS", charPerc="perc")
trackPlotTSS <- plotSummarizedCov(covSummarized)
print(trackPlotTSS)
Results
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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/plotSummarizedCov.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotSummarizedCov
> ### Title: Plots the summarized coverage in a specified range (e.g. around
> ### TSS) for the specified match sizes
> ### Aliases: plotSummarizedCov
>
> ### ** Examples
>
> #read the BAM file into a GAlignments object using
> #GenomicAlignments::readGAlignments
> #the GAlignments object should be similar to ctrlGAlignments
> data(ctrlGAlignments)
> aln <- ctrlGAlignments
> #transform the GAlignments object into a GRanges object (faster processing)
> alnGRanges <- readsToStartOrEnd(aln, what="start")
> #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
> #Please make sure that seqnames of txdb correspond to
> #the seqnames of the alignment files ("chr" particle)
> #if not rename the txdb seqlevels
> #renameSeqlevels(txdb, sub("chr", "",seqlevels(txdb)))
> #get the flanking region around the promoter of the best expressed CDSs
> oneBinRanges <- aroundPromoter(txdb, alnGRanges)
> #the read start coverage around the TSS as a percentage for all match sizes.
> covSummarized <- readStartCov(alnGRanges, oneBinRanges, matchSize="all",
+ c(-20,20), "aroundTSS", charPerc="perc")
> trackPlotTSS <- plotSummarizedCov(covSummarized)
> print(trackPlotTSS)
>
>
>
>
>
> dev.off()
null device
1
>