computeGeneGSProb {CoGAPS} | R Documentation |
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.
computeGeneGSProb( object, GStoGenes, numPerm = 500, Pw = rep(1, ncol(object@featureLoadings)), PwNull = FALSE ) ## S4 method for signature 'CogapsResult' computeGeneGSProb( object, GStoGenes, numPerm = 500, Pw = rep(1, ncol(object@featureLoadings)), PwNull = FALSE )
object |
an object of type CogapsResult |
GStoGenes |
data.frame or list with gene sets |
numPerm |
number of permutations for null |
Pw |
weight on genes |
PwNull |
- logical indicating gene adjustment |
A vector of length GSGenes containing the p-values of set membership for each gene containined in the set specified in GSGenes.