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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

roper

The goal of roper is to accurately detect differentially expressed genes in the presence of unknown forms of additional variation that remains in the RNA-Seq read count.

Installation

You can install the development version of roper from GitHub with:

# install.packages("devtools")
devtools::install_github("strug-hub/roper")

Example

This is a basic example which shows you how to solve a common problem:

library(roper)
set.seed(123)
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])
head(res)

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