map_glist: Map pathway list gene IDs to another ID type

In jdreyf/ezlimma: Streamlines and extends limma package

Map pathway list gene IDs to another ID type

Description

Map pathway list 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](https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideFrame.html?Chip2Chip_Page).

Usage

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

Arguments

G	Gene set list as returned from read_gmt.
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.

Details

Gene annotations are transformed to upper-case to avoid missing matches of different cases.

Value

Gene set list *G* with the symbols replaced by the mapped IDs.

jdreyf/ezlimma documentation built on April 28, 2024, 1:10 p.m.