Description Usage Arguments Details Value Author(s)

View source: R/calcProbeStat.R

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 |

`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.

The help file of `calcTStatFast`

has more details on the
different statistics one can calculate based on the
value specified for `ngroups`

.

A matrix with `nsim`

rows and `nrow(tab)`

columns.

Weil Lai

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