grex: Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data

In road2stat/grex: Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data

Description

Map Ensembl IDs to Entrez Gene ID, HGNC symbol, and UniProt ID, with basic annotation information such as gene type.

Usage

grex(ensembl_id)

Arguments

ensembl_id

Character vector of Ensembl IDs

Value

This function returns a data frame with the same number of rows as the length of input Ensembl IDs, containing:

• ensembl_id - Input Ensembl ID

• entrez_id - Entrez Gene ID

• hgnc_symbol - HGNC gene symbol

• hgnc_name - HGNC gene name

• cyto_loc - Cytogenetic location

• uniprot_id - UniProt ID

• gene_biotype - Gene type

The elements that cannot be mapped will be NA.

Examples

# Ensembl IDs in GTEx v6p gene count data
data("gtexv6p")
# select 100 IDs as example
id <- gtexv6p[101:200]
df <- grex(id)
# Rows that have a mapped Entrez ID
df[
  !is.na(df$"entrez_id"),
  c("ensembl_id", "entrez_id", "gene_biotype")
]

road2stat/grex documentation built on Dec. 30, 2021, 2:21 a.m.