apStats {antiProfiles}R Documentation

Compute statistics used to construct antiProfile

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 hcorrada@gmail.com

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)
 }

[Package antiProfiles version 1.28.0 Index]