filters {exonmap}R Documentation

Filter vectors of Affymetrix Exon array probeset names according to where they target

Description

Given a character vector of probeset names, filter it to keep (or exclude) those probesets that are mapped by X:Map to exons, introns, intergenic regions or are annotated as containing potentially cross-hybridizing (multitarget) probes. Functions of the form is. ... return a logical vector.

Usage

  exonic(v,exclude=FALSE,mt.rm=TRUE)
  intronic(v,exclude=FALSE,mt.rm=TRUE)
  intergenic(v,exclude=FALSE,mt.rm=TRUE)
  multitarget(v,exclude=FALSE,mt.level=1)
  is.exonic(v)
  is.intronic(v)
  is.intergenic(v)
  is.multitarget(v,mt.level=1)
  select.probewise(v,filter=c("exonic","intronic","intergenic","multitarget"),mt.rm=TRUE,mt.level=1)
  exclude.probewise(v,filter=c("exonic","intronic","intergenic","multitarget"),mt.rm=TRUE,mt.level=1)

Arguments

v A character vector of probeset names identifiers
exclude If TRUE, remove (rather than keep) matching probesets, from the list.
mt.rm If TRUE, remove multitarget probesets before returning the result
mt.level The amount of multitargeting needed before a probeset is removed. See the package vignette for more details on how this number is calculated.
filter What sort of probeset should be retained/removed?

Details

Connects to the X:Map database to retrieve data. Before these functions can be used, xmapConnect must have been called.

By default, multitarget probesets are removed.

Value

A character vector of filtered names.

Author(s)

C.J. Miller, M.J. Okoniewski

References

http://xmap.picr.man.ac.uk

See Also

xmapConnect mappings details

Examples

  if(interactive()) {
    xmapConnect()
    gene <-  probeset.to.gene(c("3743919"))
    ps   <- gene.to.probeset(gene,as.vector=TRUE)
    exonic(ps)
    intronic(ps)
    intergenic(ps)
    multitarget(ps)
    exonic(ps,exclude=TRUE)
    intronic(ps,exclude=TRUE)
    intergenic(ps,exclude=TRUE)
    multitarget(ps,exclude=TRUE,mt.level=1)
    #or
    select.probewise(ps,"exonic") #etc..
    exclude.probewise(ps,"exonic") #etc..
    is.exonic(ps)
    is.intronic(ps)
    is.intergenic(ps)
    is.multitarget(ps)
    is.multitarget(ps,mt.level=4)

  }

[Package exonmap version 2.0.03 Index]