viper (version 1.6.0)

ttestNull: Null model by sample permutation testing

Description

This function performs sample permutation and t-test to generate a null model

Usage

ttestNull(x, ...)
"ttestNull"(x, y, per = 1000, repos = TRUE, seed = 1, cores = 1, verbose = TRUE)
"ttestNull"(x, pheno, group1, group2, per = 1000, repos = TRUE, seed = 1, verbose = TRUE)

Arguments

x

ExpressionSet object or Matrix containing the test dataset

...

Additional parameters added to keep compatibility

y

Matrix containing the reference dataset

per

Integer indicating the number of permutations

repos

Logical, whether the permutations should be performed with reposition

seed

Integer indicating the seed for the permutations, 0 for disable it

cores

Integer indicating the number of cores to use (set to 1 in windows systems)

verbose

Logical, whether progression messages should be printed in the terminal

pheno

Character string indicating the phenotype data to use

group1

Vector of character strings indicating the category from phenotype pheno to use as test group

group2

Vector of character strings indicating the category from phenotype pheno to use as control group

Value

Matrix of z-scores with genes in rows and permutations in columns

See Also

msviper, viper

Examples

data(bcellViper, package="bcellViper")
d1 <- exprs(dset)
dnull <- ttestNull(d1[, 1:10], d1[, 11:20], per=100)
dim(dnull)
plot(density(dnull))
data(bcellViper, package="bcellViper")
dnull <- ttestNull(dset, "description", "CB", "CC", per=100)
dim(dnull)
plot(density(dnull))