normalMM: Performing empirical Bayes modeling on limma results

In CEDA: CRISPR Screen and Gene Expression Differential Analysis

Performing empirical Bayes modeling on limma results

Description

This function perform an empirical Bayes modeling on log fold ratios and return the posterior log fold ratios.

Usage

normalMM(data, theta0, n.b = 5, d = 10)

Arguments

data	A numeric matrix containing limma results and log2 gene expression levels that has a column nameed 'lfc' and a column named 'exp.level.log2'
theta0	Standard deviation of log2 fold changes under permutations
n.b	Number of bins, default is 5 bins
d	Number of times for fitting mixture model using different starting values, default is 10

Value

A numeric matrix containing limma results, RNA expression levels, posterior log2 fold ratio, log p-values, and estimates of mixture model

CEDA documentation built on May 29, 2024, 7:44 a.m.