annmap.filters: annmap 'filter' functions

In annmap: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Description

Functions to filter exon array probeset names by the genome features they correspond to.

Usage

  exonic( probesets, exclude=FALSE )
  hasProbes( probesets, num.probes=4, exclude=FALSE )
  hasProbesAtleast( probesets, num.probes=4, exclude=FALSE )
  hasProbesIn( probesets, num.probes=c( 1, 2, 3, 4 ), exclude=FALSE )
  hasProbesBetween( probesets, min.probes=1, max.probes=4, exclude=FALSE, inclusive=TRUE )
  intergenic( probesets, exclude=FALSE )
  intronic( probesets, exclude=FALSE )
  isExonic( probesets )
  isIntergenic( probesets )
  isIntronic( probesets )
  isUnreliable( probesets )
  unreliable( probesets, exclude=FALSE )

Arguments

probesets	A vector of probesets to filter
num.probes	The required number of probes to have in the probeset
exclude	If FALSE, then return a list containing only those probesets matching the filter. If TRUE then return only those that don\'t match the filter
min.probes	Minimum number of probes within a probeset
max.probes	Maximum number of probes within a probeset
inclusive	Whether to include the extremes of the range in the search or not

Details

Probesets are classified according to whether they map to known genes. The function exonic filters for probesets for which all probes match once (and only once) to the genome, and every probe hits an exon. Note that this means that a probeset that hits more than one exon, will be flagged as exonic. All probes in intronic probesets hit the genome once (and once only), and all probes hit a gene - however one or more probes hit an intron. intergenic probesets hit the genome once (and once only) but one or more probes miss a gene compeletely. unreliable probesets comprise those that have at least one probe that does not align to the genome, or one or more probes that align at multiple loci (multiply targeted).

The functions is.exonic, is.intronic and is.intergenic, return a logical vector classifying the supplied probesets.

The functions has.probes, has.probes.in and has.probes.between can be used to filter a set of probesets according to the numbers of probes they contain.

Author(s)

Tim Yates Crispin J. Miller

See Also

annmapTo
annmapDetails
annmapAll
annmapRange
annmapFilters

Examples

  if(interactive()){
    annmapConnect()
    ps <- geneToProbeset(symbolToGene("TP53"))
    exonic(ps)
    intronic(ps)
    intergenic(ps)
    unreliable(ps)
    isExonic(ps)
    isIntronic(ps)
    isIntergenic(ps)
    isUnreliable(ps)
    hasProbes(ps)
    hasProbesIn(ps,1:3)
    hasProbesBetween(ps,2,3)
    hasProbesAtleast(ps,4)
  }

annmap documentation built on Nov. 8, 2020, 7:43 p.m.