R/lineup: detecting and correcting sample mix-ups

R/lineup is an R package with tools for detecting and correcting sample mix-ups between two sets of measurements, such as between gene expression data on two tissues.

This is particularly aimed at eQTL data for an experimental cross.

Installation

Install the R/lineup package from CRAN:

install.packages("lineup")

Alternatively, install it from R universe:

install.packages("lineup", repos=c("https://kbroman.r-universe.dev",
                                   "https://cloud.r-project.org"))

Or use remotes to install it from its GitHub source:

install.packages("remotes")
remotes::install_github("kbroman/lineup")

Vignette

A vignette describing the use of the package is available on the web. Or view it from within R by loading the package and then using the vignette() function.

library(lineup2)
vignette("lineup", package="lineup")

Citation

To cite R/lineup in publications use

• Broman KW, Keller MP, Broman AT, Kendziorski C, Yandell BS, Sen Ś, Attie AD (2015) Identification and correction of sample mix-ups in expression genetic data: A case study. G3 5:2177-2186 doi:10.1534/g3.115.019778

License

This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3