DEXSeq (version 1.18.4)

findOverlaps: Methods from GRanges overlaps for the DEXSeq object

Description

This function generates an MA plot.

Usage

"subsetByOverlaps"( query, subject, maxgap = 0L,  minoverlap = 1L, type = c("any", "start", "end", "within", "equal"), ignore.strand = FALSE )
  "findOverlaps"( query, subject, maxgap = 0L,  minoverlap = 1L, type = c("any", "start", "end", "within", "equal"), ignore.strand = FALSE )

Arguments

query

Either a DEXSeqResults object.

subject

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

  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( query=dxr, subject=interestingRegion )
  findOverlaps( query=dxr, subject=interestingRegion )