Get the gene position orders for output of OrthoFinder

Get the gene position orders without considering the strand info.

getHomologListForOrthoFinder(orthologs, marts)

Arguments

orthologs

The output of orthologPairsFromOrthoFinder.

marts

a list of object of class Mart.

Value

A list of list with gene ranks named by the chromosome names.

Examples

path <- system.file('extdata/orthofinder/Danio_rerio.GRCz11.pep.all.tsv.gz',
                  package='geneClusterPattern')
orthologs <- orthologPairsFromOrthoFinder(path)
annoGR_list <- readRDS(
     system.file('extdata/orthofinder/grange.obj.rds',
                  package='geneClusterPattern'))
homologs <- getHomologListForOrthoFinder(orthologs, annoGR_list[-1])