genomicElementUpSetR {ChIPpeakAnno} | R Documentation |
Prepare data for upset plot for genomic element distribution
genomicElementUpSetR( peaks, TxDb, seqlev, ignore.strand = TRUE, breaks = list(distal_upstream = c(-1e+05, -10000, -1, 1), proximal_upstream = c(-10000, -5000, -1, 1), distal_promoter = c(-5000, -2000, -1, 1), proximal_promoter = c(-2000, 200, -1, 0), `5'UTR` = fiveUTRsByTranscript, `3'UTR` = threeUTRsByTranscript, CDS = cds, exon = exons, intron = intronsByTranscript, gene_body = genes, immediate_downstream = c(0, 2000, 1, 1), proximal_downstream = c(2000, 5000, 1, 1), distal_downstream = c(5000, 1e+05, 1, 1)) )
peaks |
peak list, GRanges object or a GRangesList. |
TxDb |
an object of |
seqlev |
sequence level should be involved. Default is all the sequence levels in intersect of peaks and TxDb. |
ignore.strand |
logical. Whether the strand of the input ranges should be ignored or not. Default=TRUE |
breaks |
list. A list for labels and sets for the genomic elements. The element could be an S4 method for signature 'TxDb' or a numeric vector with length of 4. The three numbers are c(upstream point, downstream point, promoter (-1) or downstream (1), remove gene body or not (1: remove, 0: keep)). |
The data will be calculated by for each breaks. No precedence will be considered.
list of data for plot.
if (interactive() || Sys.getenv("USER")=="jianhongou"){ data(myPeakList) if(require(TxDb.Hsapiens.UCSC.hg19.knownGene)){ seqinfo(myPeakList) <- seqinfo(TxDb.Hsapiens.UCSC.hg19.knownGene)[seqlevels(myPeakList)] myPeakList <- GenomicRanges::trim(myPeakList) myPeakList <- myPeakList[width(myPeakList)>0] x <- genomicElementUpSetR(myPeakList, TxDb.Hsapiens.UCSC.hg19.knownGene) library(UpSetR) upset(x$plotData, nsets=13, nintersects=NA) } }