tmodImportMSigDB: Import data from MSigDB
In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

tmodImportMSigDB

R Documentation

Import data from MSigDB

Description

Import data from an MSigDB file in either XML or GMT format

Usage

tmodImportMSigDB(
  file = NULL,
  format = "xml",
  organism = "Homo sapiens",
  fields = c("STANDARD_NAME", "CATEGORY_CODE", "SUB_CATEGORY_CODE", "EXACT_SOURCE",
    "EXTERNAL_DETAILS_URL")
)

Arguments

`file`	The name of the file to parse
`format`	Format (either "xml" or "gmt")
`organism`	Select the organism to use. Use "all" for all organisms in the file (only for "xml" format; default: "Homo sapiens")
`fields`	Which fields to import to the MODULES data frame (only for "xml" format)

Details

This command parses a file from MSigDB. Both XML and the MSigDB-specific "GMT" format are supported (however, the latter is discouraged, as it contains less information).

Value

A tmod object

Examples

## Not run: 
## First, download the file "msigdb_v7.5.1.xml" 
## from http://www.broadinstitute.org/gsea/downloads.jsp
msig <- tmodImportMSigDB("msigdb_v7.5.1.xml")

## End(Not run)

tmod documentation built on March 31, 2023, 9 p.m.