addGeneSetDescription: Utility function which adds the biological description of the...

In MLP: MLP

Description

Utility function which adds the biological description of the gene sets as a column to the return value of the MLP function (data frame)

Usage

addGeneSetDescription(object, geneSetSource = NULL)

Arguments

object

object of class 'MLP' as produced by the 'MLP' function

geneSetSource

source to be used to construct the list of pathway categories; for public data sources, the user can specify a string (one of 'GOBP', 'GOMF', 'GOCC', 'KEGG' or 'REACTOME') and BioC packages will be used to construct the list of pathway categories; for non-public data sources, the user can pass the pathway data as a dataframe with (at least) the following four columns: PATHWAYID, TAXID, PATHWAYNAME and GENEID. It is assumed all columns are of type character. The 'geneSetSource' argument should be the same as the argument provided to the getGeneSets function; defaults to NULL

Value

the data frame as returned by MLP enriched with an additional column geneSetDescription, providing a concise description of the gene set

See Also

MLP

MLP documentation built on Nov. 8, 2020, 8:23 p.m.