apStats {antiProfiles} | R Documentation |
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
apStats(e, cl, tiss = NULL, minL = 10, cutoff = 5, OnCutoff = 2.54)
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 |
An object of class SuccsStats
Hector Corrada Bravo hcorrada@gmail.com
AntiProfileStats
for the type of
object returned. buildAntiProfile
to
construct anti-profiles with objects returned by this
function.
if (require(antiProfilesData)) { data(apColonData) colonStats = apStats(exprs(apColonData), pData(apColonData)$Status) }