genomicElementUpSetR: Genomic Element data for upset plot

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

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)
  }
}

jianhong/ChIPpeakAnno documentation built on Aug. 16, 2024, 12:40 a.m.