rope: Robust profile likelihood-based differential expression...

In strug-hub/roper: Robust Profile Likelihood Method for Differential Expression Analysis in R

Robust profile likelihood-based differential expression analysis

Description

Fit a robust profile likelihood ratio test for a working Poisson log-linear model.

Usage

rope(datmat, X_model, x_PI_idx)

Arguments

datmat	A matrix of filtered RNA-seq counts.
X_model	A numerical design matrix contains DE experiment group (parameter of interest) and other covariates
x_PI_idx	An integer indicates the column index of the parameter of interest, usually the DE experiment group.

Value

A data frame with columns contain the DE result of log fold change, unadjusted and adjusted log likelihood ratio, adjustment factors, p-values and Benjamini & Hochberg adjusted p-values.

Examples

count <- matrix(rnbinom(n = 5e4, mu = 100, size = 1 / 0.5), ncol = 50)
mod <- model.matrix(~ gl(n = 2, k = 25))
res <- rope(datmat = count, X_model = mod, x_PI_idx = dim(mod)[2])
res

strug-hub/roper documentation built on March 26, 2023, 10:01 p.m.