sum_groups: Sum Expression of Orthologs

In othomantegazza/crossr: Functions For Cross Species Quantitative Transcriptomics

Sum Expression of Orthologs

Description

sum_groups takes an expression matrix and a list of orthogroups. It sums the expression of all the genes in one orthogroup across the samples and outputs a orthogroup-wise expression matrix

Usage

sum_groups(eset, ogroups, mc.cores = 1)

Arguments

eset	a data.frame with the a gene-wise or transcript-wise expression matrix
ogroups	a list of orthogroups, the gene names in the list should match the row.names of the datasets
mc.cores	numeric, the number of threads

Details

Some step are considerably slow and are parallelized with the function mclapply from the package parallel the number of threads defaults to 1. The gene/transcripts IDs in the orthogroups are searched for a match in the rownames of the expressiom matrix using grep

othomantegazza/crossr documentation built on Feb. 1, 2023, 7:44 a.m.