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Permutation Test for CIBERSORT

Source: R/CIBERSORT.R
doPerm.Rd

Performs permutation-based sampling to generate an empirical null distribution of correlation coefficients for p-value calculation in CIBERSORT analysis. Randomly samples from the mixture data to create null distributions.

Usage

doPerm(perm, X, Y, absolute, abs_method, seed = NULL)

Arguments

perm

Integer. Number of permutations to perform (\(\ge\)100 recommended for reliable p-value estimation).

X

Matrix or data frame containing signature matrix (predictor variables).

Y

Numeric vector containing the mixture sample expression.

absolute

Logical indicating whether to use absolute space for weights.

abs_method

String specifying the method for absolute space weights: `"sig.score"` or `"no.sumto1"`.

seed

Integer. Random seed for reproducibility. If NULL (default), uses current random state.

Value

List containing:

dist

Numeric vector of correlation coefficients from permutations

Examples

X <- matrix(rnorm(100), nrow = 10)
Y <- rnorm(10)
result <- doPerm(100, X, Y, absolute = FALSE, abs_method = "sig.score")