simple_gsea: Do a simplified version of GSEA with most default parameters

In kaigu1990/siGSEA: A simple GSEA tool for expression data

Description

'simple_gsea' is used to output result of GSEA. You just need to import expression matrix and gene set as element files. Then you have to provide the group info of samples. See this examples for more information

Usage

simple_gsea(dataexpr, group, geneset, gsminsize = 15, gsmaxsize = 500,
  nperm = 1000)

Arguments

dataexpr	Matrix or dataframe of expression data (rows are genes and columns are samples)
group	A vector which distinguishs some samples to others(Just support two phenotypes)
geneset	Gene set databases in Molecular Signatures Database (MSigDB)
gsminsize	Minimum size (in genes) for database gene sets to be considered (default: 15)
gsmaxsize	Maximum size (in genes) for database gene sets to be considered (default: 500)
nperm	Number of random permutations (default: 1000)

Value

gseaResult object

Examples

data <- read.table(file = "expression.txt", sep = "\t", header = T, row.names = 1, stringsAsFactors = F, quote = "")
group <- c(rep("m", 15), rep("f", 17))
class <- factor(group)
gene_set <- readLines("C1.gmt")
res <- simple_gsea(dataexpr = data, group = class, geneset = gene_set, gsminsize = 15, gsmaxsize = 500, nperm = 1000)

kaigu1990/siGSEA documentation built on May 3, 2019, 4:04 p.m.