standardise_gene_names: Standardises the range of gene names used in GenBank

In EvolEcolGroup/mtDNAcombine: R package to download, combine, and curate sequences from public databases

Description

standardise_gene_names

Usage

standardise_gene_names(df_to_update, names_to_replace)

Arguments

df_to_update	data frame with a column name $gene_name. Any instances of multiple names for what is a single gene within this column will be standardised
names_to_replace	user provided .csv file or default .csv file ("gene_nomenclature_correction.csv") which lists alternative names for each gene. One gene for each column, header is new standardised gene name option, rest of column is filled with erroneous versions of the gene name.

Details

This function turns an extensive but not exhaustive list of possible gene name synonyms/miss-spellings/alternative abbreviations into standardised format.

Function loads either user provided .csv file or default .csv file ("gene_nomenclature_correction.csv") and uses gsub to replace all alternative gene name patterns given with a single, standard, gene name.

EvolEcolGroup/mtDNAcombine documentation built on July 8, 2021, 10:30 p.m.