findOverlaps {DEXSeq} | R Documentation

## Methods from GRanges overlaps for the DEXSeq object

### Description

This function generates an MA plot.

### Usage

      ## 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

      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 )

[Package DEXSeq version 1.38.0 Index]