tmod (version 0.50.13)

tmodImportMSigDB: 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")
)

Value

A tmod object

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).

Examples

if (FALSE) {
## First, download the file "msigdb_v7.5.1.xml" 
## from http://www.broadinstitute.org/gsea/downloads.jsp
msig <- tmodImportMSigDB("msigdb_v7.5.1.xml")
}