parallel_doperm: Parallel Permutation Test for CIBERSORT

In IOBR: Immune Oncology Biological Research

Parallel Permutation Test for CIBERSORT

Description

Parallel version of doPerm. Performs permutation-based sampling and runs the CoreAlg function iteratively using multiple CPU cores to accelerate computation. This function generates an empirical null distribution of correlation coefficients for p-value calculation in CIBERSORT analysis.

Usage

parallel_doperm(
  perm1,
  X1,
  Y1,
  absolute1,
  abs_method1,
  num_cores1 = 2,
  seed = NULL
)

Arguments

perm1	Integer. Number of permutations to perform (\ge100 recommended).
X1	Matrix or data frame. Signature matrix (cell type GEP barcode).
Y1	Matrix. Mixture file containing gene expression profiles.
absolute1	Logical. Whether to run in absolute mode (default: FALSE).
abs_method1	String. Method for absolute mode: 'sig.score' or 'no.sumto1'.
num_cores1	Integer. Number of CPU cores for parallel computation (default: 2).
seed	Integer. Random seed for reproducibility. If NULL (default), uses current random state. Set to a specific value (e.g., 123) for reproducible results across runs.

Details

This function utilizes the foreach and doParallel packages to distribute permutation iterations across multiple cores. It automatically handles cluster setup/teardown via on.exit() to prevent resource leaks.

Note: Windows users may experience slower performance due to socket-based parallelization (PSOCK) versus forking on Unix systems.

Value

List containing:

dist

Numeric vector of correlation coefficients from permutations, representing the empirical null distribution.

See Also

doPerm for the sequential version, CoreAlg, CIBERSORT

Examples

# Simulate data
set.seed(123)
X <- matrix(rnorm(1000), nrow = 100)
Y <- matrix(rnorm(500), nrow = 100)
rownames(X) <- rownames(Y) <- paste0("Gene", 1:100)
colnames(X) <- paste0("Cell", 1:10)
colnames(Y) <- paste0("Sample", 1:5)

# Run parallel permutation test
result <- parallel_doperm(
  perm1 = 10, X1 = X, Y1 = Y,
  absolute1 = FALSE, abs_method1 = "sig.score", num_cores1 = 1
)
if (!is.null(result)) str(result$dist)

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