sigPathway (version 1.40.0)

calcTNullFast: Compute Null T Distribution for Each Gene

Description

Computes a null t distribution for each gene by permuting the phenotypes.

Usage

calcTNullFast(tab, phenotype, nsim, ngroups = 2, allphenotypes = FALSE)

Arguments

tab

a numeric matrix of expression values, with the rows and columns representing probe sets and sample arrays, respectively

phenotype

a numeric (or character if ngroups >= 2) vector indicating the phenotype

nsim

an integer indicating the number of permutations to use

ngroups

an integer indicating the number of groups in the expression matrix

allphenotypes

a boolean indicating whether the function should consider all possible permutations of the phenotype, including the original, non-permuted phenotype

Value

A matrix with nsim rows and nrow(tab) columns.

Details

Similar to calcTStatFast but calculates t-statistics over permuted phenotypes. If allphenotypes == FALSE, then any permutation that has a permuted phenotype equal to the original phenotype will be repermuted. For example, all the possible permutations for phenotype == c(0,0,1,1) are c(0,0,1,1), c(0,1,0,1), c(1,0,1,0), c(1,0,0,1), c(0,1,1,0), and c(1,1,0,0). If allphenotypes == FALSE, then the results will not include values from the c(0,0,1,1) case. The help file of calcTStatFast has more details on the different statistics one can calculate based on the value specified for ngroups.