meta.test {metaseqR} | 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

        meta.test(cp.list,
            meta.p = c("simes", "bonferroni", "fisher", "dperm.min",
            "dperm.max", "dperm.weight", "fperm", "whitlock",
            "minp", "maxp", "weight", "pandora", "none"), counts,
            sample.list, statistics, stat.args, libsize.list,
            nperm = 10000, weight = rep(1/length(statistics),
            length(statistics)), reprod=TRUE, multic = FALSE)

### Arguments

`cp.list` | a named list whose names are the contrasts requested from metaseqr. Each member is a p-value matrix whose colnames are the names of the statistical tests applied to the data. See the main `metaseqr` help page.
`meta.p` | the p-value combination method to use. See the main `metaseqr` help page.
`counts` | the normalized and possibly filtered read counts matrix. See the main `metaseqr` help page.
`sample.list` | the list containing condition names and the samples under each condition. See the main `metaseqr` help page.
`statistics` | the statistical algorithms used in metaseqr. See the main `metaseqr` help page.
`stat.args` | the parameters for each statistical argument. See the main `metaseqr` help page.
`libsize.list` | a list with library sizes. See the main `metaseqr` 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.
`reprod` | create reproducible permutations when `meta.p="dperm.min"`, `meta.p="dperm.max"` or `meta.p="dperm.weight"`. Ideally one would want to create the same set of indices for a given dataset so as to create reproducible p-values. If `reprod=TRUE`, a fixed seed is used by `meta.perm` for all the datasets analyzed with `metaseqr`. If `reprod=FALSE`, then the p-values will not be reproducible, although statistical significance is not expected to change for a large number of resambling. Finally, `reprod` can be a numeric vector of seeds with the same length as `nperm` so that the user can supply his/her own seeds.
`multic` | use multiple cores to execute the premutations. This is an external parameter and implies the existence of multicore package in the execution environment. See the main `metaseqr` help page.

### 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

    # Not yet available

[Package metaseqR version 1.28.0 Index]