readStartCov {RiboProfiling} | R Documentation |
Read start coverage around the TSS on the predifined CDSs
readStartCov(alnGRanges, oneBinRanges, matchSize = "all", fixedInterval, renameChr, charPerc = "perc")
alnGRanges |
A GRanges object containing the alignment information. In order to improve the performance transform the GAlignments BAM object into a GRanges object containing cigar match size as metadata. |
oneBinRanges |
A GRanges object. Transform the gene GRangesList into one big GRanges object. Add the info on the cds_id. |
matchSize |
either "all" or a vector of read match sizes. If matchSize <- "all", then all the reads are used to compute the coverage. If the matchSize is a vector of read match sizes, the summarized coverage is reported per match size and for the sum up. |
fixedInterval |
a numeric vector with the extremities of the interval. Ex. fixedInterval <- c(-20,20) or fixedInterval <- c(0,40) ... |
renameChr |
a character object. It contains the name to be given to the new summarized coverage interval. Ex. renameChr <- "aroundTSS" the summarized region around the TSS. |
charPerc |
a character object. Either "perc" (the default) or "sum" for percentage of counts per position or the sum of counts per position. |
a list of GRanges objects (for each matchSize chosen). It contains the summarized coverage for the specified read match sizes.
#read the BAM 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, percBestExpressed=0.01) #the coverage in the TSS flanking region for the summarized read match sizes listPromoterCov <- readStartCov( alnGRanges, oneBinRanges, matchSize="all", fixedInterval=c(-20, 20), renameChr="aroundTSS", charPerc="perc" )