Description Usage Arguments Value Examples

With null distributions estimated using the `generateNull()`

function, p-values are estimated using a one-tailed test. A minimum p-value
of 1/B can be achieved with B permutations.

1 |

`permuteResult` |
A matrix, null distributions for each sample generated
using the |

`scoredf` |
A dataframe, the scored results of samples under test
generated using the |

`subSamples` |
A vector of sample labels/indices that will be used to subset the score matrix. All samples will be scored if not provided |

Estimated p-values for enrichment of the signature in each sample. A p-value of 1/B indicates that the estimated p-value is less than or equal to 1/B.

1 2 3 4 5 6 7 8 9 10 11 12 | ```
ranked <- rankGenes(toy_expr_se)
scoredf <- simpleScore(ranked, upSet = toy_gs_up, downSet = toy_gs_dn)
# find out what backends can be registered on your machine
BiocParallel::registered()
# the first one is the default backend, and it can be changed explicitly.
# See vignette for more details
permuteResult = generateNull(upSet = toy_gs_up, downSet = toy_gs_dn, ranked,
B =10, seed = 1, useBPPARAM = NULL)
# call the permutation function to generate the empirical scores
# for B times.
pvals <- getPvals(permuteResult,scoredf)
``` |

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