ttestNull {viper} | R Documentation |
This function performs sample permutation and t-test to generate a null model
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)
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 |
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) 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))