R: Graphs of sample read counts (quality assesment)
countsPlot
R Documentation
Graphs of sample read counts (quality assesment)
Description
Graphs of sample read counts (quality assesment)
Usage
countsPlot(listCounts, ixCounts, log2Bool)
Arguments
listCounts
a list of data.frame objects.
It contains the counts on the genomic features.
Each data.frame in the list should have the same number of columns.
ixCounts
a numeric (a vector of integers).
It contains the index of the columns containing counts in the dataFrame.
log2Bool
a numeric, either 0 or 1.
0 (default) for no log2 transformation and 1 for log2 transformation.
Value
A list of pairs and boxplots between the counts data in each data.frame.
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
#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)
#get the per transcript relative position of start and end codons
cdsPosTransc <- orfRelativePos(cds, exonGRanges)
#compute the counts on the different features after applying
#the specified shift value on the read start along the transcript
countsData <-
countShiftReads(
exonGRanges[names(cdsPosTransc)],
cdsPosTransc,
alnGRanges,
-14
)
#now make the plots
listCountsPlots <- countsPlot(
list(countsData[[1]]),
grep("_counts$", colnames(countsData[[1]])),
1
)
listCountsPlots
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/countsPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: countsPlot
> ### Title: Graphs of sample read counts (quality assesment)
> ### Aliases: countsPlot
>
> ### ** 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
>
> #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)
>
> #get the per transcript relative position of start and end codons
> cdsPosTransc <- orfRelativePos(cds, exonGRanges)
>
> #compute the counts on the different features after applying
> #the specified shift value on the read start along the transcript
> countsData <-
+ countShiftReads(
+ exonGRanges[names(cdsPosTransc)],
+ cdsPosTransc,
+ alnGRanges,
+ -14
+ )
Warning message:
In countShiftReads(exonGRanges[names(cdsPosTransc)], cdsPosTransc, :
Param motifSize should be an integer! Accepted values 3, 6 or 9. Default value is 3.
>
> #now make the plots
> listCountsPlots <- countsPlot(
+ list(countsData[[1]]),
+ grep("_counts$", colnames(countsData[[1]])),
+ 1
+ )
> listCountsPlots
[[1]]
[[1]][[1]]
[[2]]
>
>
>
>
>
> dev.off()
null device
1
>