tissueSpecAntiprofile-class: A gene expression anti-profile using tissue-specific regions

In antiProfiles: Implementation of gene expression anti-profiles

Description

This class encapsulates anti-profiles with tissue-specific normal expression regions. Objects of this class should be built from AntiProfileStats objects using the buildAntiProfile method. Anti-profile scores can be computed for new samples using the apCount method.

Usage

  ## Accessors

  ## S4 method for signature 'TissueSpecAntiProfile'
getProbesetIds(object) 
  ## S4 method for signature 'TissueSpecAntiProfile'
getNormalRegions(object)
  getNormalTissueRegions(object)

Arguments

object

Object of class TissueSpecAntiProfile

Accessors

In the following code object is a TissueSpecAntiProfile object.

getProbesetIds:

vector of Affymetrix ids for probesets included in the anti-profile (character)

getNormalRegions:

median and upper boundary of normal expression regions (numeric matrix of dimension s-by-2, where s is the size of the anti-profile)

getNormalTissueRegions:

median and upper boundary of normal expression regions (numeric array of dimension s-by-2-by-t, where s is the size of the anti-profile, and t the number of normal tissues used in the anti-profile)

Author(s)

Hector Corrada Bravo [e-mail]

See Also

AntiProfileStats for the class of objects from which anti-profiles are built. buildAntiProfile for the method used to construct objects of this class. apCount for the function used to calculate anti-profile scores from objects of this class. #'

Examples

if (require(antiProfilesData)) {
    data(apColonData)
    # fake tissues
    tissue=rep(c("colon","lung"), len=length(sampleNames(apColonData)))
    tissStats=apStats(exprs(apColonData), pData(apColonData)$Status, tiss=tissue, minL=3)
    tissAP=buildAntiProfile(tissStats, sigsize=10)
    show(tissAP)

    head(getProbesetIds(tissAP))
    head(getNormalRegions(tissAP))
    head(getNormalTissueRegions(tissAP))
  }

antiProfiles documentation built on Nov. 8, 2020, 6:43 p.m.