stuart

stuart is a R package used to analyze whole genome genotyping results of animals used by crossing laboratory strains. It is particularly useful for F2 or N2 individuals as it allows to filter the markers in the arrays that can or cannot be used for further analysis from a genetic point of view. Mrkers will be selected depending on their proportion of each genotype, correspondance between F2 or N2 individuals alleles and parental strains alleles, etc.

Installation

You can install the released version of stuart from GitLab, by dowloading the latest tar.gz file and installing it with:

install.packages(path_to/stuart_X.Y.Z.tar.gz, repos = NULL, type="source")

Or directly in R with:

devtools::install_gitlab(repo="mouselab/stuart",host="gitlab.pasteur.fr")

Example

To see an example of the use of stuart package with miniMUGA array, consult the package vignette.