mmGeneSetTest: multiple-multiple geneSetTests

In rmflight/ccPaper: work for categoryCompare paper revisions

Description

The default geneSetTest in limma will only do a single index and a single test. This function allows one to pass in a set of indices, and do all three tests (up, down, mixed).

Usage

  mmGeneSetTest(index, statistics, ranks.only = FALSE,
    do.parallel = TRUE, ...)

Arguments

index	list of indices generated by symbols2indices
statistics	the statistics to use
ranks.only	whether to rank only, default is FALSE
do.parallel	use multiple cores to do everything
...	other parameters for geneSetTest

Details

Note that the function will try to do all three of up, down and mixed, but if there is no sign (i.e. F-statistic instead of t-statistic) the function will only do a test for "mixed"

Value

data.frame of p-values for each alternative test

rmflight/ccPaper documentation built on May 27, 2019, 9:31 a.m.