antiprofile-class: A gene expression anti-profile

In antiProfiles: Implementation of gene expression anti-profiles

Description

This class encapsulates anti-profiles. 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

  getProbesetIds(object) 
  getNormalRegions(object)

Arguments

object

Object of class (or inheriting from) AntiProfile

Accessors

In the following code object is a AntiProfile 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)

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)
    colonStats=apStats(exprs(apColonData), pData(apColonData)$Status)
    colonAP = buildAntiProfile(colonStats, tissueSpec=FALSE, sigsize=10)
    show(colonAP)

    head(getProbesetIds(colonAP))
    head(getNormalRegions(colonAP))
  }

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