Assess orthogroup inference based on functional annotation
Source:R/homology_detection.R
assess_orthogroups.Rd
Assess orthogroup inference based on functional annotation
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.