exp_genes2orthogroups {BioNERO} | R Documentation |
For a given list of expression data, this function replaces genes with their corresponding orthogroups to allow inter-species comparisons.
exp_genes2orthogroups(explist = NULL, og = NULL, summarize = "median")
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". |
List of expression data frames for each species with expression summarized at the orthogroup level.
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")