GetOrthologs: Find orthologs in other species by gene/protein IDs

In markgene/gorthoR: R package

Description

Find orthologs in other species given IDs and their source species taxonomy ID

Usage

GetOrthologs(source.taxid = source.taxid, target.taxid = target.taxid,
  query.id = query.id, id.type = c("entrez_gene_id", "ensembl_pep_id",
  "ensembl_gene_id"), clusterid.cidx = 1, taxid.cidx = 2, id.cidx = 3,
  no.id = NA, diagnose = FALSE)

Arguments

query.id	query IDs
id.type	which type of IDs are used: Entrez Gene ID, Ensembl gene ID, Ensembl peptide ID
source.taxid	NCBI taxonomy ID of source species
target.taxid	NCBI taxonomy ID of target species

Value

list of elements each of which is a vector of Ensembl peptide IDs in target species

Author(s)

Mark J Chen [e-mail]

Examples

GetOrthologs(source.taxid=4932, target.taxid=4896, query.id=c("YIL106W", "YOR358W"), id.type="ensembl_pep_id")
GetOrthologs(source.taxid=4932, target.taxid=4896, query.id=c(854700, 854540), id.type="entrez_gene_id")

markgene/gorthoR documentation built on May 21, 2019, noon