ttestNull-methods: Null model by sample permutation testing

In viper: Virtual Inference of Protein-activity by Enriched Regulon analysis

Description

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

Usage

ttestNull(x, ...)

## S4 method for signature 'matrix'
ttestNull(x, y, per = 1000, repos = TRUE,
  seed = 1, cores = 1, verbose = TRUE)

## S4 method for signature 'ExpressionSet'
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))

viper documentation built on Nov. 8, 2020, 7:37 p.m.