readPathways {netDx} | R Documentation

## Parse GMT file and return pathways as list

### Description

Parse GMT file and return pathways as list

### Usage

    readPathways(fname, MIN_SIZE = 10L, MAX_SIZE = 200L,
      EXCLUDE_KEGG = TRUE, IDasName = FALSE, verbose = TRUE,
      getOrigNames = FALSE)

### Arguments

`fname` | (char) path to pathway file in gmt format pathway score to include pathway in the filter list
`MIN_SIZE` | (integer) min num genes allowed in a pathway. Pathways with fewer number of genes are excluded from the output list
`MAX_SIZE` | (integer) max num genes allowed in a pathway. Pathways with gene counts greater than this are excluded from the output list
`EXCLUDE_KEGG` | (boolean) If TRUE exclude KEGG pathways. Our experience has been that some KEGG gene sets are to broad to be physiologically relevant
`IDasName` | (boolean) Value for key in output list. If TRUE, uses db name and ID as name (e.g. KEGG:hsa04940) If FALSE, pathway name.
`verbose` | (logical) print detailed messages
`getOrigNames` | (logical) when TRUE also returns a mapping of the cleaned pathway names to the original names

### Details

The GMT file format currently supported should match the ones found at http://downloads.baderlab.org. The original GMT file format is: <set name><set description><member 1><member 2>...<member N>, one row per set, with values tab-delimited. The version at baderlab.org has additional unique formatting of the <set name> column as follows: <pathway_full_name> This function requires the specific formatting of the first column to assign the key name of the output list (see `useIDasName` argument).

### Value

Depends on value of getOrigNames. If FALSE (Default), list with pathway name as key, vector of genes as value. If TRUE, returns list of length two, (1) geneSets: pathway-gene mappings as default, (2) pNames: data.frame with original and cleaned names.

### Examples

    pathFile <- fetchPathwayDefinitions()
    pathwayList    <- readPathways(pathFile)

[Package netDx version 1.0.3 Index]