Import data from MSigDB — tmodImportMSigDB • tmod

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)

Value

A tmod object

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")
}