conv_ids_full: Converting gene IDS using orgDB and maRt

In Troshchk/bioEAT: bioExploreAnnotateTranslate

Description

This function returns a dataframe with translated IDs and NA row for the not anootated genes.

Usage

conv_ids_full(
  input,
  db_cluster_profiler,
  from_cluster_profiler,
  mart,
  from_mart
)

Arguments

input	vector of IDs
db_cluster_profiler	annotation clusterProfiler database
from_cluster_profiler	input clusterProfiler ID type: ENSEMBL, ENTREZID, SYMBOL
mart	annotation mart
from_mart	input maRt ID type: ensembl_gene_id, external_gene_name, entrezgene_id

Details

This function takes a vector of IDs and translated them from the input format to the output format using the selected orgDB. The IDs not found by OrgDB are further annotated by maRt. If the ID was not found it will be at the end of the output dataframe with NAs. This function works only with the IDs: ENSEMBL ID, SYMBOL, ENTREZID In case the orgDB is not installed before launching the function, the function will exit with error.

Value

dataframe with the ENSEMBL ID, SYMBOL, ENTREZID, GENENAME(description); NAs are not dropped

Examples

conv_ids_full(rownames(dataNorm_df), "org.Mmu.eg.db", "ENSEMBL",
"mmulatta_gene_ensembl", "ensembl_gene_id")
conv_ids_full(c("IFNA13", "SLC2A3", "CD45RA", "CDY2A", "IGHM", "IGKC"), "org.Mmu.eg.db",  
"SYMBOL", "mmulatta_gene_ensembl", "external_gene_name")

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