doPerm: Permutation Test for CIBERSORT

In IOBR: Immune Oncology Biological Research

Permutation Test for CIBERSORT

Description

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 (\ge100 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

# Simulate data
set.seed(123)
X <- matrix(rnorm(100), nrow = 10)
rownames(X) <- paste0("Gene", 1:10)
colnames(X) <- paste0("Cell", 1:10)
Y <- rnorm(10)
names(Y) <- paste0("Gene", 1:10)

# Run permutation test
result <- doPerm(10, X, Y, absolute = FALSE, abs_method = "sig.score")
if (!is.null(result)) str(result)

IOBR documentation built on May 30, 2026, 5:07 p.m.