make.permutation: Create counts matrix permutations

In pmoulos/metaseqR: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

Description

This function creates a permuted read counts matrix based on the contrast argument (to define new virtual contrasts of the same number) and on the sample.list to derive the number of samples for each virtual condition.It is a helper for the meta.perm function.

Usage

    make.permutation(counts, sample.list, contrast,
        repl = FALSE)

Arguments

counts	the gene read counts matrix.
sample.list	the list containing condition names and the samples under each condition.
contrast	the contrasts vector. See the main metaseqr help page.
repl	the same as the replace argument in sample function.

Value

A list with three members: the matrix of permuted per sample read counts, the virtual sample list and the virtual contrast to be used with the stat.* functions.

Author(s)

Panagiotis Moulos

Examples

data("mm9.gene.data",package="metaseqR")
per <- make.permutation(mm9.gene.counts,sample.list.mm9,
    "e14.5_vs_adult_8_weeks")

pmoulos/metaseqR documentation built on Dec. 21, 2020, 6:19 a.m.