map_t2g: Map pathway term to gene IDs to another ID type
In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

map_t2g

R Documentation

Map pathway term to gene IDs to another ID type

Description

Map pathway term to gene with old gene IDs (e.g. entrez IDs) to another ID type (e.g. gene symbols) using a table with both annotation types. The original IDs can be separated within a column of annot with a string, e.g. " /// ". The other IDs should be the rownames of annot. The idea for this is based on the Gene Set Enrichment Analysis (GSEA) utility chip2chip.

Usage

map_t2g(
  t2g,
  annot,
  sep.str = " /// ",
  symbol.col = "Gene.Symbol",
  fixed = FALSE
)

Arguments

`t2g`	TERM TO GENE mapping, a data.frame of 2 column with term and gene
`annot`	annotation for the features that has a column of the same type as in gene set list G.
`sep.str`	strings that separates symbols if there are multiple symbols for a feature.
`symbol.col`	column name or index for the symbol column in annot.
`fixed`	logical passed to `strsplit`; if `TRUE`, match `sep.str` exactly, otherwise use regular expression.