Read Orthologues results as a list This function is under-development.

Read Orthologues results as a list This function is under-development.

fromOrthogroups(orthogroups, annoGR_list, query_species = 1, split = ", ")

Arguments

orthogroups

A dataframe with the gene ids for each orthologues group

annoGR_list

A GRangesList object with the gene information. The names of each element should be contain all the gene ids saved in the orthogroups parameter. For each element, the 'gene_name' should be available in the metadata.

query_species

The species used as queryGR in getGeneCluster.

split

character vector used to split the gene ids in the dataframe of orthogroups parameter.

Value

a list of queryGR and homologsList used by getGeneCluster.

Examples

orthogroups <- read.delim(
     system.file('extdata/orthofinder/Orthogroups.tsv.gz',
                  package='geneClusterPattern'),
     row.names=1)
annoGR_list <- readRDS(
     system.file('extdata/orthofinder/grange.obj.rds',
                  package='geneClusterPattern'))
colnames(orthogroups) <- names(annoGR_list)
hres <- fromOrthogroups(orthogroups, annoGR_list)