symbol_to_entrez_id: Function to map gene symbols to entrez gene ids. The input...

Description Usage Arguments Value

View source: R/id_mapping.R

Description

Function to map gene symbols to entrez gene ids. The input gene symbols can be of a variety of formats (eg, REFSEQ, ENSEMBL) provided the symbol type is present as a column name in the provided AnnotationDbi dataset. If any symbol maps to multiple entrez gene ids, the entrez ids are collapsed into a single string. The function returns a vector of entrez ids, with the order of the output matching exactly with the order of the input. Any symbol that can"t be mapped to an entrez id returns with the value NA

Usage

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symbol_to_entrez_id(gene_symbols = character(0),
  symbol_type = "SYMBOL", entrezgene_db = NULL,
  collapse_character = "|")

Arguments

gene_symbols

vector of some type of gene symbol (eg, Ensembl, Refseq, HGNC)

symbol_type

the type of gene symbol used (should be a colname for the entrezgene_db)

entrezgene_db

a database object for use in mapping symbol to entrezGene id.

collapse_character

a single character for collapsing multiple ids into a single entry.

Value

a vector of the same length as gene_symbols containing the entrez ids that correspond to the input gene_symbols.


russHyde/miiq documentation built on Dec. 25, 2019, 10:56 a.m.