s2i: Convert between gene symbol, Wormbase ID, and sequence name

In AlexWeinreb/wbData: Download And Use WormBase Data

Convert between gene symbol, Wormbase ID, and sequence name

Description

Convert between gene symbol, Wormbase ID, and sequence name

Usage

s2i(symbol, geneIDs, warn_missing = FALSE)

i2s(gene_id, geneIDs, warn_missing = FALSE)

wb_seq2id(seq_id, geneIDs, warn_missing = FALSE)

wb_id2seq(gene_id, geneIDs, warn_missing = FALSE)

wb_seq2name(seq_id, geneIDs, warn_missing = FALSE)

wb_symbol2seq(symbol, geneIDs, warn_missing = FALSE)

Arguments

symbol	gene symbols (e.g. aap-1).
geneIDs	Translation table generated with 'load_gene_ids()'.
warn_missing	If TRUE, a warning is issued when a gene symbol was not found.
gene_id	Wormbase gene ID (e.g. WBGene00000001).
seq_id	sequence ID (e.g. F27C8.1)

Details

These functions convert between different gene identifiers using a preloaded translation table. 's2i' and 'i2s' are the most commonly used, a longer name would be 'wb_symbol2id' and 'wb_id2symbol'. The gene 'name' is the gene 'symbol' if it exists, and the sequence ID otherwise.

Value

The corresponding IDs.

Examples

gids <- wb_load_gene_ids("WS277")
s2i(c("unc-10", "aap-1"), gids)

AlexWeinreb/wbData documentation built on April 3, 2025, 1:24 p.m.