aroundPromoter {RiboProfiling} | R Documentation |
Returns the flank size around the TSS for the x % CDSs
aroundPromoter(txdb, alnGRanges, percBestExpressed, flankSize)
txdb |
a TxDb object containing the annotations info to intersect with the alignment files. |
alnGRanges |
A GRanges object containing the alignment information. In order to improve the performance of this function the GAlignments BAM object should be transformed into a GRanges object containing the cigar match size information as metadata. |
percBestExpressed |
a numeric [between 0 and 1]. The percentage of the best expressed CDSs on which to plot the coverage around the TSS. Necessary if the shiftValue parameter must be estimated. Default value 0.03 (3%). |
flankSize |
a numeric positive integer. How many bp left and right of the TSS should the coverage be performed? Ex. flankSize <- 20 |
A GRanges object containing the 1 bp ranges for the selected CDSs in the TSS defined flanking region.
#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)