methods-gr: Methods from GRanges overlaps for the DEXSeq object

Description Usage Arguments Examples

Description

This function generates an MA plot.

Usage

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  ## S4 method for signature 'DEXSeqResults,GenomicRanges'
subsetByOverlaps( x, ranges, maxgap = -1L, 
    minoverlap = 0L, type = c("any", "start", "end", "within", "equal"),
    ignore.strand = FALSE )

  ## S4 method for signature 'DEXSeqResults,GenomicRanges'
findOverlaps( query, subject, maxgap = -1L, 
    minoverlap = 0L, type = c("any", "start", "end", "within", "equal"),
    ignore.strand = FALSE )

Arguments

query, x

Either a DEXSeqResults object.

subject, ranges

A GRanges or GRangesList object.

maxgap, minoverlap, type

See findOverlaps in the IRanges package for a description of these arguments.

ignore.strand

See findOverlaps in the GenomicRanges package for a description of this.

Examples

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  data(pasillaDEXSeqDataSet, package="pasilla")
  dxd <- estimateSizeFactors( dxd )
  dxd <- estimateDispersions( dxd )
  dxd <- testForDEU( dxd )
  dxr <- DEXSeqResults( dxd )

  interestingRegion = GRanges("chr2L", IRanges(start=3872658, end=3875302))

  subsetByOverlaps( x=dxr, ranges=interestingRegion )
  findOverlaps( query=dxr, subject=interestingRegion )

areyesq89/DEXSeq documentation built on June 26, 2020, 2:31 a.m.