metaseqR (version 1.12.2)

make.permutation: Create counts matrix permutations

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.

Examples

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