Collapse gene-level expression data to orthogroup level

For a given list of expression data, this function replaces genes with their corresponding orthogroups to allow inter-species comparisons.

Usage

exp_genes2orthogroups(explist = NULL, og = NULL, summarize = "median")

Arguments

explist

List of expression data frames or SummarizedExperiment objects.

og

Data frame of 3 columns corresponding to orthogroup, species ID, and gene ID, respectively. Species IDs must be the same as the names of the expression list.

summarize

Centrality measure to summarize multiple paralogous genes in the same orthogroup. One of "median" or "mean". Default: "median".

Value

List of expression data frames for each species with expression summarized at the orthogroup level.

Examples

# \donttest{
data(og.zma.osa)
data(zma.se)
data(osa.se)
explist <- list(zma = zma.se,
                osa = osa.se)
og <- og.zma.osa
exp_ortho <- exp_genes2orthogroups(explist, og, summarize = "mean")
# }