exp_genes2orthogroups {BioNERO} | R Documentation

## Collapse gene-level expression data to orthogroup level

### Description

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

    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")

[Package BioNERO version 1.0.4 Index]