geneSetsList: Convert gene set data in gmt file to R list

In mGSZ: Gene set analysis based on GSZ-scoring function and asymptotic p-value

Description

Converts gene set data in gmt file to R list readable by mGSZ program

Usage

geneSetsList(data)

Arguments

data	Gene set data in gmt file format

Value

Gene set data in list format with gene set name as list names

Author(s)

Pashupati Mishra, Petri Toronen

Examples

## gene.sets <- geneSetsList(filename.gmt) ##

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GSA
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: MASS
Loading required package: ismev
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-24. For overview type 'help("mgcv-package")'.

mGSZ documentation built on May 2, 2019, 5:53 p.m.