CalcClusterEnrichPvals: Calculate cluster enrichment with logistic regression

In yanwu2014/perturbLM: A lightweight R package that uses linear models to analyze the effects of chemical/genetic perturbations, conditions, and disease states on single gene expression.

Calculate cluster enrichment with logistic regression

Description

Calculate cluster enrichment with logistic regression

Usage

CalcClusterEnrichPvals(
  design.mat,
  cov.mat,
  clusters,
  alpha,
  lambda.use,
  n.rand = 1000,
  n.cores = 8,
  ctrl = NULL
)

Arguments

design.mat	Design matrix for regression
cov.mat	Matrix of covariates to regress out
clusters	Cluster assignments
alpha	Elasticnet ratio: (0 is fully L2, 1 fully is L1)
lambda.use	Shrinkage parameter
n.rand	Number of permutations
n.cores	Number of multiprocessing cores
ctrl	Control genotype to compare all other genotypes to (e.g. NTC, AAVS)

Value

Matrix of regression coefficients

yanwu2014/perturbLM documentation built on Aug. 24, 2023, 2:28 p.m.