getGenomePairs: Retrieves the pairwise relations among two genomes

In klarakaleb/roma: R wrapper for the OMA REST API

Retrieves the pairwise relations among two genomes

Description

This function retrieves the pairwise relations among two genomes from the OMA Browser database. The relations are orthologs in case the genomes are different and "close paralogs" and "homoeologs" in case they are the same.

Usage

getGenomePairs(genome_id1, genome_id2, chr1 = NULL, chr2 = NULL,
  rel_type = NULL, ...)

Arguments

genome_id1	an identifier for the first genome, which can be either its taxon id or UniProt species code
genome_id2	an an identifier for the second genome, which can be either its taxon id or UniProt species code
chr1	the chromosome of interest for the first genome
chr2	the chromosome of interest for the second genome
rel_type	the pairs relationship type
...	qwargs

Details

By using the parameters chr1 and chr2, one can limit the relations to a certain chromosome for one or both genomes. The id of the chromosome corresponds to the chromosome ids from the getGenome result.

The rel_type parameter further limits the returned relations to a specific subtype of orthologs (i.e. "1:1", "1:n", "m:1", "m:n") or - within a genome to either "close paralogs" or "homeologs".

Value

a dataframe containing information about both the entries in the orthologous pair and their relationship

Examples

getGenomePairs(genome_id1='YEAST',genome_id2='ASHGO')

klarakaleb/roma documentation built on April 21, 2024, 8:39 a.m.