bootstrapTtest {viper} | R Documentation |
This function generates a bootstrapped signature matrix by t-test
bootstrapTtest(x, ...) ## S4 method for signature 'matrix' bootstrapTtest(x, y, per = 100, seed = 1, cores = 1, verbose = TRUE) ## S4 method for signature 'ExpressionSet' bootstrapTtest(x, pheno, group1, group2, per = 100, seed = 1, verbose = TRUE)
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 |
group2 |
Vector of character strings indicating the category from phenotype |
Matrix of z-scores with genes in rows and permutations in columns
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, ]))