calcTNullFast: Compute Null T Distribution for Each Gene
In sigPathway: Pathway Analysis

Description Usage Arguments Details Value Author(s)

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

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

`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

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.