Get the gene positions for homologs — getHomologGeneList • geneClusterPattern

Get the gene positions without considering the strand info.

getHomologGeneList(species, mart, ensembl_gene_ids, ...)

Arguments

species: The target species for homologs query.
mart: object of class Mart.
ensembl_gene_ids: Ensembl gene ids.
...: Parameters could be used by useEnsembl except `biomart`.

Value

A list of GRanges objects with gene positions.

Examples

if(interactive()){
  ## Ensembl server may not response
  library(biomaRt)
  fish <- readRDS(system.file('extdata', 'fish.rds',
                            package = 'geneClusterPattern'))
  ensembl_gene_ids <- names(fish[seqnames(fish)=='24'])
  species <- c('hsapiens', 'mmusculus')
  fish_mart <- useMart("ENSEMBL_MART_ENSEMBL", "drerio_gene_ensembl")
  homologs <- getHomologGeneList(species, fish_mart, ensembl_gene_ids)
}