assignChromosomeRegion: Summarize peak distribution over exon, intron, enhancer,...

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

Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR

Description

Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR

Usage

assignChromosomeRegion(
  peaks.RD,
  exon,
  TSS,
  utr5,
  utr3,
  proximal.promoter.cutoff = c(upstream = 2000, downstream = 100),
  immediate.downstream.cutoff = c(upstream = 0, downstream = 1000),
  nucleotideLevel = FALSE,
  precedence = NULL,
  TxDb = NULL
)

Arguments

peaks.RD	peaks in GRanges: See example below
exon	exon data obtained from getAnnotation or customized annotation of class GRanges containing additional variable: strand (1 or + for plus strand and -1 or - for minus strand). This parameter is for backward compatibility only. TxDb should be used instead.
TSS	TSS data obtained from getAnnotation or customized annotation of class GRanges containing additional variable: strand (1 or + for plus strand and -1 or - for minus strand). For example, data(TSS.human.NCBI36),data(TSS.mouse.NCBIM37), data(TSS.rat.RGSC3.4) and data(TSS.zebrafish.Zv8). This parameter is for backward compatibility only. TxDb should be used instead.
utr5	5 prime UTR data obtained from getAnnotation or customized annotation of class GRanges containing additional variable: strand (1 or + for plus strand and -1 or - for minus strand). This parameter is for backward compatibility only. TxDb should be used instead.
utr3	3 prime UTR data obtained from getAnnotation or customized annotation of class GRanges containing additional variable: strand (1 or + for plus strand and -1 or - for minus strand). This parameter is for backward compatibility only. TxDb should be used instead.
proximal.promoter.cutoff	Specify the cutoff in bases to classify proximal promoter or enhencer. Peaks that reside within proximal.promoter.cutoff upstream from or overlap with transcription start site are classified as proximal promoters. Peaks that reside upstream of the proximal.promoter.cutoff from gene start are classified as enhancers. The default is upstream 2000 bases and downstream 100 bases.
immediate.downstream.cutoff	Specify the cutoff in bases to classify immediate downstream region or enhancer region. Peaks that reside within immediate.downstream.cutoff downstream of gene end but not overlap 3 prime UTR are classified as immediate downstream. Peaks that reside downstream over immediate.downstreatm.cutoff from gene end are classified as enhancers. The default is upstream 0 bases and downstream 1000 bases.
nucleotideLevel	Logical. Choose between peak centric and nucleotide centric view. Default=FALSE
precedence	If no precedence specified, double count will be enabled, which means that if a peak overlap with both promoter and 5'UTR, both promoter and 5'UTR will be incremented. If a precedence order is specified, for example, if promoter is specified before 5'UTR, then only promoter will be incremented for the same example. The values could be any conbinations of "Promoters", "immediateDownstream", "fiveUTRs", "threeUTRs", "Exons" and "Introns", Default=NULL
TxDb	an object of TxDb

Value

A list of two named vectors: percentage and jaccard (Jaccard Index). The information in the vectors:

list("Exons")	Percent or the picard index of the peaks resided in exon regions.
list("Introns")	Percent or the picard index of the peaks resided in intron regions.
list("fiveUTRs")	Percent or the picard index of the peaks resided in 5 prime UTR regions.
list("threeUTRs")	Percent or the picard index of the peaks resided in 3 prime UTR regions.
list("Promoter")	Percent or the picard index of the peaks resided in proximal promoter regions.
list("ImmediateDownstream")	Percent or the picard index of the peaks resided in immediate downstream regions.
list("Intergenic.Region")	Percent or the picard index of the peaks resided in intergenic regions.

The Jaccard index, also known as Intersection over Union. The Jaccard index is between 0 and 1. The higher the index, the more significant the overlap between the peak region and the genomic features in consideration.

Author(s)

Jianhong Ou, Lihua Julie Zhu

References

1. Zhu L.J. et al. (2010) ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 2010, 11:237doi:10.1186/1471-2105-11-237

2. Zhu L.J. (2013) Integrative analysis of ChIP-chip and ChIP-seq dataset. Methods Mol Biol. 2013;1067:105-24. doi: 10.1007/978-1-62703-607-8_8.

See Also

genomicElementDistribution, genomicElementUpSetR, binOverFeature, binOverGene, binOverRegions

Examples

if (interactive() || Sys.getenv("USER")=="jianhongou"){
    ##Display the list of genomes available at UCSC:
    #library(rtracklayer)
    #ucscGenomes()[, "db"]
    ## Display the list of Tracks supported by makeTxDbFromUCSC()
    #supportedUCSCtables()
    ##Retrieving a full transcript dataset for Human from UCSC
    ##TranscriptDb <- 
    ##     makeTxDbFromUCSC(genome="hg19", tablename="ensGene")
    if(require(TxDb.Hsapiens.UCSC.hg19.knownGene)){
      TxDb <- TxDb.Hsapiens.UCSC.hg19.knownGene
      exons <- exons(TxDb, columns=NULL)
      fiveUTRs <- unique(unlist(fiveUTRsByTranscript(TxDb)))
      Feature.distribution <- 
          assignChromosomeRegion(exons, nucleotideLevel=TRUE, TxDb=TxDb)
      barplot(Feature.distribution$percentage)
      assignChromosomeRegion(fiveUTRs, nucleotideLevel=FALSE, TxDb=TxDb)
      data(myPeakList)
      assignChromosomeRegion(myPeakList, nucleotideLevel=TRUE, 
                             precedence=c("Promoters", "immediateDownstream", 
                                          "fiveUTRs", "threeUTRs", 
                                          "Exons", "Introns"), 
                             TxDb=TxDb)
    }
}

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