metaTest {metaseqR2} | R Documentation

## Meta-analysis using several RNA-Seq statistics

### Description

This function calculates the combined p-values when multiple statistical algorithms are applied to the input dataset. It is a helper and it requires very specific arguments so it should not be used individually

### Usage

        metaTest(cpList,
            metaP = c("simes", "bonferroni", "fisher", "dperm_min",
            "dperm_max", "dperm_weight", "fperm", "whitlock",
            "minp", "maxp", "weight", "pandora", "none"), counts,
            sampleList, statistics, statArgs, libsizeList,
            nperm = 10000, weight = rep(1/length(statistics),
            length(statistics)), rc = NULL)

### Arguments

`cpList` | a named list whose names are the contrasts requested from metaseqr2. Each member is a p-value matrix whose colnames are the names of the statistical tests applied to the data. See the main `metaseqr2` help page.
`metaP` | the p-value combination method to use. See the main `metaseqr2` help page.
`counts` | the normalized and possibly filtered read counts matrix. See the main `metaseqr2` help page.
`sampleList` | the list containing condition names and the samples under each condition. See the main `metaseqr2` help page.
`statistics` | the statistical algorithms used in metaseqr2. See the main `metaseqr2` help page.
`statArgs` | the parameters for each statistical argument. See the main `metaseqr2` help page.
`libsizeList` | a list with library sizes. See the main `metaseqr2` and the `stat*` help pages.
`nperm` | the number of permutations (Monte Carlo simulations) to perform.
`weight` | a numeric vector of weights for each statistical algorithm.
`rc` | the fraction of the available cores to use in a multicore system.

### Details

Ideally one would want to create the same set of indices for a given dataset so as to create reproducible p-values. To achieve this, use the `set.seed` function prior to any calculations. When metaseqR2 is loaded, the random seed is set to `42`.

### Value

A named list with combined p-values. The names are the contrasts and the list members are combined p-value vectors, one for each contrast.

### Author(s)

Panagiotis Moulos

### Examples

    cpList <- list(a=matrix(runif(100),50,2))
    metaP <- metaTest(cpList,"simes")

[Package metaseqR2 version 1.0.11 Index]