calcTNullFast {sigPathway} | R Documentation

## 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

### 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`.

### Value

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

### Author(s)

Weil Lai

[Package sigPathway version 1.8.0 Index]