viper (version 1.6.0)

bootstrapTtest: Bootstrapped signature by t-test

Description

This function generates a bootstrapped signature matrix by t-test

Usage

bootstrapTtest(x, ...)
"bootstrapTtest"(x, y, per = 100, seed = 1, cores = 1, verbose = TRUE)
"bootstrapTtest"(x, pheno, group1, group2, per = 100, seed = 1, verbose = TRUE)

Arguments

x

Matrix containing the test dataset

...

Additional parameters added to keep compatibility

y

Matrix containing the reference dataset

per

Integer indicating the number of permutations

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-based systems)

verbose

Logical whether progress should be reported

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

Examples

data(bcellViper, package="bcellViper")
d1 <- exprs(dset)
sig <- bootstrapTtest(d1[, 1:10], d1[, 11:20], per=100)
dim(sig)
plot(density(sig[1907, ]))
data(bcellViper, package="bcellViper")
sig <- bootstrapTtest(dset, "description", "CB", "N", per=100)
dim(sig)
plot(density(sig[1907, ]))