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

Description Usage Arguments Value Author(s) Examples

View source: R/getOrthologs.R

Description

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

Usage

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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 [email protected]

Examples

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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, 2017, 7:42 p.m.