toTable: Table with top gene sets

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

Description

Table with top gene sets

Usage

toTable(mGSZobj, sample.perm.table = FALSE, method = c("mGSZ", "mGSA", "mAllez", "WRS", "SS", "SUM", "KS", "wKS"), no.top.sets = 10)

Arguments

mGSZobj	mGSZ object
sample.perm.table	TRUE for table of top gene sets based on sample permutation when both gene and sample permutations were used.
method	Method for which table for top gene sets is required (Required only when other methods were used for the gene set analysis)
no.top.sets	Number of top gene sets in the table

Value

A table with top gene sets

Author(s)

Pashupati Mishra, Petri Toronen

References

Mishra Pashupati, Toronen Petri, Leino Yrjo, Holm Liisa. Gene Set Analysis: Limitations in popular existing methods and proposed improvements (Not yet published) http://ekhidna.biocenter.helsinki.fi/downloads/pashupati/mGSZ.html

See Also

mGSZ

Examples

gene.names <- paste("g",1:1000, sep = "")

# create random gene expression data matrix

set.seed(100)
expr.data <- matrix(rnorm(1000*50),ncol=50)
rownames(expr.data) <- gene.names
b <- matrix(2*rnorm(2500),ncol=25)
ind <- sample(1:100,replace=FALSE)
expr.data[ind,26:50] <- expr.data[ind,26:50] + b

sample.labels <- rep(1:2,c(25,25))

# create random gene sets

gene.sets <- vector("list", 100)
for(i in 1:length(gene.sets)){
	gene.sets[[i]] <- sample(gene.names, size = 20)
}
names(gene.sets) <- paste("set", as.character(1:100), sep="")

mGSZ.obj <- mGSZ(expr.data, gene.sets, sample.labels, perm.number = 100)
top.mGSZ.sets <- toTable(mGSZ.obj, no.top.sets = 10) 

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