genomicElementUpSetR {ChIPpeakAnno} | R Documentation

## Genomic Element data for upset plot

### Description

Prepare data for upset plot for genomic element distribution

### Usage

    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))
    )

### Arguments

`peaks` | peak list, GRanges object or a GRangesList.
`TxDb` | an object of `TxDb`
`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)).

### Details

The data will be calculated by for each breaks. No precedence will be considered.

### Value

list of data for plot.

### Examples

    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)
      }
    }

[Package ChIPpeakAnno version 3.24.2 Index]