genomicElementDistribution: Genomic Element distribution

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 distribution

Description

Plot pie chart for genomic element distribution

Usage

genomicElementDistribution(
  peaks,
  TxDb,
  seqlev,
  nucleotideLevel = FALSE,
  ignore.strand = TRUE,
  promoterRegion = c(upstream = 2000, downstream = 100),
  geneDownstream = c(upstream = 0, downstream = 1000),
  labels = list(geneLevel = c(promoter = "Promoter", geneDownstream = "Downstream",
    geneBody = "Gene body", distalIntergenic = "Distal Intergenic"), ExonIntron = c(exon
    = "Exon", intron = "Intron", intergenic = "Intergenic"), Exons = c(utr5 = "5' UTR",
    utr3 = "3' UTR", CDS = "CDS", otherExon = "Other exon"), group = c(geneLevel =
    "Transcript Level", promoterLevel = "Promoter Level", Exons = "Exon level",
    ExonIntron = "Exon/Intron/Intergenic")),
  labelColors = c(promoter = "#E1F114", geneBody = "#9EFF00", geneDownstream = "#57CB1B",
    distalIntergenic = "#066A4B", exon = "#6600FF", intron = "#8F00FF", intergenic =
    "#DA00FF", utr5 = "#00FFDB", utr3 = "#00DFFF", CDS = "#00A0FF", otherExon =
    "#006FFF"),
  plot = TRUE,
  keepExonsInGenesOnly = TRUE,
  promoterLevel
)

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.
nucleotideLevel	Logical. Choose between peak centric and nucleotide centric view. Default=FALSE
ignore.strand	logical. Whether the strand of the input ranges should be ignored or not. Default=TRUE
promoterRegion	numeric. The upstream and downstream of genes to define promoter region.
geneDownstream	numeric. The upstream and downstream of genes to define gene downstream region.
labels	list. A list for labels for the genomic elements.
labelColors	named character vector. The colors for each labels.
plot	logic. Plot the pie chart for the genomic elements or not.
keepExonsInGenesOnly	logic. Keep the exons within annotated gene only.
promoterLevel	list. The breaks, labels, and colors for divided range of promoters. The breaks must be from 5' -> 3' and the percentage will use the fixed precedence 3' -> 5'

Details

The distribution will be calculated by geneLevel, ExonIntron, and Exons The geneLevel will be categorized as promoter region, gene body, gene downstream and distal intergenic region. The ExonIntron will be categorized as exon, intron and intergenic. The Exons will be categorized as 5' UTR, 3'UTR and CDS. The precedence will follow the order of labels defination. For example, for ExonIntron, if a peak overlap with both exon and intron, and exon is specified before intron, then only exon will be incremented for the same example.

Value

Invisible 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]
    genomicElementDistribution(myPeakList, 
        TxDb.Hsapiens.UCSC.hg19.knownGene)
    genomicElementDistribution(myPeakList, 
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        nucleotideLevel = TRUE)
    genomicElementDistribution(myPeakList, 
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        promoterLevel=list(
        #from 5' -> 3', fixed precedence 3' -> 5'
        breaks = c(-2000, -1000, -500, 0, 100),
        labels = c("upstream 1-2Kb", "upstream 0.5-1Kb", 
                   "upstream <500b", "TSS - 100b"),
        colors = c("#FFE5CC", "#FFCA99", 
                   "#FFAD65", "#FF8E32")))
  }
}

jianhong/ChIPpeakAnno documentation built on Feb. 2, 2024, 3:26 p.m.