check_gene_db: Check gene names against NCBI database and fix nomenclature

In toddknutson/toddr: A collection of functions for RNAseq, scRNAseq, variant calling, and other bioinformatics methods.

Check gene names against NCBI database and fix nomenclature

Description

Check gene names against NCBI database and fix nomenclature

Usage

check_gene_db(gene_vector, gene_db)

Arguments

gene_vector	Required. Character vector of input gene names. These can be slightly incorrect in their capitalization or be gene aliases.
gene_db	Required. Tibble data frame of the GENE database downloaded from NCBI. See below for details. How to download gene_db: url <- "https://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz" url <- "https://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz" download.file(url, basename(url), method = "wget") gene_db <- read_tsv(gzfile(basename(url)))

Value

None

Examples

## Not run: 
genes_clean <- check_gene_db(genes_dirty, gene_db)

## End(Not run)

toddknutson/toddr documentation built on Aug. 28, 2023, 2:45 a.m.