convert: Convert gene annotation

In Dudemanguy/geneConvert: Simple and fast batch gene id conversion.

Description

Main function used to convert the inputed genes from one set of annotations to another.

Usage

convert(genes, "Homo sapiens", "symbol", "description", full=FALSE)

Arguments

genes	A character vector of genes
organism	The name of the organism
input	The annotation type of the inputted genes
output	The annotation type of the output
full	A boolean controlling whether to return all annotations

Details

organism must be the proper, scientific name. However, there are three shortcuts hardcoded for homo_sapiens, mus_musculus, and rattus_norvegicus. These would be human, mouse, and rat respectively. If you want to convert annotation for a different organism, please add it first using the addNewOrganism function.

input and output must match the field names in the SQL table. Valid names are symbol, geneid, description, geneloc, transcript, protein, ensembl, and date. Note that output can accept multilength character vectors.

If enabled, full will return all annotations for the queried genes instead of just the specified output.

Examples

output <- convert(genes, "human", "symbol", "ensembl")

Dudemanguy/geneConvert documentation built on Dec. 5, 2019, 12:46 a.m.