inferorg: Infer the organism and ID format given a list of genes.

In camlab-bioml/inferorg: Infer organism and identifier type given a list of genes

Description

Infer the organism and ID format given a list of genes.

Usage

inferorg(gene_vec)

Arguments

gene_vec

Vector of input gene IDs to guess the organism and format of

Details

This function takes in a vector of gene IDs, and guesses the format, which is one of:

• symbol (e.g. PTPRC)

• ensgene (e.g. ENSG00000081237)

• entrez (e.g. 5788)

along with the organism, which is one of:

• human

• mouse

• fruit_fly

• macaque

• worm

• chicken

• rat

In addition, a confidence score for both the organism and format is computed (see vignette for details).

Value

A list with four entries:

• organism The inferred organism.

• format The inferred ID format.

• confidence_organism The confidence in the organism inferred, between 0 and 1.

• confidence_format The confidence in the format inferred, between 0 and 1.

Examples

genes <- c("HLA-A", "HLA-B", "HLA-C")
inferorg(genes)

camlab-bioml/inferorg documentation built on Feb. 14, 2022, 12:44 a.m.