translate: Finding gene homologs

In Troshchk/bioEAT: bioExploreAnnotateTranslate

Description

This function returns a dataframe with homolog IDs and NA row for the genes with no homologs.

Usage

translate(
  input,
  taxid,
  from_id = "ENTREZID",
  homologeneFile,
  db_cluster_profiler = NULL,
  from_mart = NULL,
  mart = NULL
)

Arguments

input	vector of IDs
taxid	taxonomy ID of the target species – https://www.ncbi.nlm.nih.gov/Taxonomy/Browser
from_id	input ID type with default "ENTREZID", other possible: "ENSEMBL", "SYMBOL"
homologeneFile	homology table – https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data
db_cluster_profiler	annotation clusterProfiler database for the input organism; necessary only if the input ID is not ENTREZ ID
from_mart	input maRt ID type for the input organism: ensembl_gene_id, external_gene_name, entrezgene_id; necessary only if the input ID is not ENTREZ ID
mart	annotation maRt for the input organism; necessary only if the input ID is not ENTREZ ID

Details

This function takes a vector of IDs. If the IDs are not ENTREZ IDs, they are converted to the ENTREZ ID format. Next, the homologs of the IDs are found using the homologeneFile. The IDs which were not coverted and the IDs without homologs are returned.

Value

dataframe with the input IDs(if different from ENTREZ ID), input ENTREZ ID, output ENTREZ ID of the target organism; NAs are not dropped

Examples

translate(rownames(dataNorm_df), 9606, homologeneFile = file)
translate(rownames(dataNorm_df), 9606,
    from_id = "ENSEMBL", homologeneFile = file,
    db_cluster_profiler = "org.Mmu.eg.db", mart = "mmulatta_gene_ensembl",
    from_mart = "ensembl_gene_id"
)

Troshchk/bioEAT documentation built on Dec. 18, 2021, 5:13 p.m.