tmodImportMSigDB: Import data from MSigDB

Description Usage Arguments Details Value Examples

View source: R/importexport.R

Description

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

Usage

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

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## Not run: 
## First, download the file "msigdb_v5.0.xml" from http://www.broadinstitute.org/gsea/downloads.jsp
msig <- tmodImportMSigDB( "msigdb_v5.0.xml" )

## End(Not run)

tmod documentation built on Oct. 23, 2020, 6:12 p.m.