apStats: Compute statistics used to construct antiProfile

In antiProfiles: Implementation of gene expression anti-profiles

Description

This function calculates normal ranges of expressions and variance ratios for all probesets. To create an anti-profile, call buildAntiProfile on the output of this function

Usage

  apStats(e, cl, tiss = NULL, minL = 10, cutoff = 5,
    OnCutoff = 2.54)

Arguments

e	matrix of gene expression, with one column per sample
cl	vector of normal/cancer indicators as 0/1
tiss	vector of tissue types for each sample
minL	minimum number of samples of a given tissue/class to compute stats
cutoff	median absolute deviation multiplier used to determine proportion of samples within normal range of expression
OnCutoff	gene expression barcode z-score to determine if a gene is expressed

Value

An object of class SuccsStats

Author(s)

Hector Corrada Bravo [e-mail]

See Also

AntiProfileStats for the type of object returned. buildAntiProfile to construct anti-profiles with objects returned by this function.

Examples

if (require(antiProfilesData)) {
   data(apColonData)
   colonStats = apStats(exprs(apColonData), pData(apColonData)$Status)
 }

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