computeGeneGSProb {CoGAPS} | R Documentation |
Compute Gene Probability
computeGeneGSProb(Amean, Asd, GSGenes, Pw = rep(1, ncol(Amean)), numPerm = 500, PwNull = FALSE)
Amean |
A matrix mean values |
Asd |
A matrix standard deviations |
GSGenes |
data.frame or list with gene sets |
Pw |
weight on genes |
numPerm |
number of permutations for null |
PwNull |
- logical indicating gene adjustment |
Computes the p-value for gene set membership using the CoGAPS-based
statistics developed in Fertig et al. (2012). This statistic refines set
membership for each candidate gene in a set specified in GSGenes
by
comparing the inferred activity of that gene to the average activity of the
set.
A vector of length GSGenes containing the p-values of set membership for each gene containined in the set specified in GSGenes.
data('SimpSim') computeGeneGSProb(SimpSim.result$Amean, SimpSim.result$Asd, GSGenes=GSets[[1]], numPerm=500)