meta.test: Meta-analysis using several RNA-Seq statistics

Description Usage Arguments Value Author(s) Examples

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

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    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

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pmoulos/metaseqR documentation built on May 9, 2019, 12:58 a.m.