assess_orthogroups: Assess orthogroup inference based on functional annotation

In almeidasilvaf/cogeqc: Systematic quality checks on comparative genomics analyses

Assess orthogroup inference based on functional annotation

Description

Assess orthogroup inference based on functional annotation

Usage

assess_orthogroups(
  orthogroups = NULL,
  annotation = NULL,
  correct_overclustering = TRUE
)

Arguments

orthogroups	A 3-column data frame with columns Orthogroup, Species, and Gene. This data frame can be created from the 'Orthogroups.tsv' file generated by OrthoFinder with the function read_orthogroups().
annotation	A list of 2-column data frames with columns Gene (gene ID) and Annotation (annotation ID). The names of list elements must correspond to species names as in the second column of orthogroups. For instance, if there are two species in the orthogroups data frame named "SpeciesA" and "SpeciesB", annotation must be a list of 2 data frames, and each list element must be named "SpeciesA" and "SpeciesB".
correct_overclustering	Logical indicating whether to correct for overclustering in orthogroups. Default: TRUE.

Value

A data frame.

Examples

data(og)
data(interpro_ath)
data(interpro_bol)
# Subsetting annotation for demonstration purposes.
annotation <- list(Ath = interpro_ath[1:1000,], Bol = interpro_bol[1:1000,])
assess <- assess_orthogroups(og, annotation)

almeidasilvaf/cogeqc documentation built on Jan. 29, 2024, 7:20 a.m.