SolangeD/RSambada: Processing Pipeline for 'SamBada' from Pre- To Post-Processing

Processing pipeline for 'SamBada' from pre- to post-processing. 'SamBada' is a landscape genomic software designed to run univariate or multivariate logistic regression between the presence of a genotype and one or several environmental variables. See Stucki (2017) <doi:10.1111/1755-0998.12629> and <https://github.com/Sylvie/sambada>. The package provides functions that can be classified into four categories: 1) Install 'SamBada' 2) Preprocessing (prepare genomic file into standards compatible with 'SamBada' and apply quality-control; retrieve environmental conditions at sampling location; prepare environmental file including removal of correlated variables and computation of population structure) 3) Processing (run 'SamBada' on multiple cores using 'Supervision') 4) Post-processing (calculate p-values and q-values, produce interactive Manhattan plots and query 'Ensembl' database, produce maps).

Getting started

Package details

AuthorSolange Duruz, Sylvie Stucki, Oliver Selmoni, Elia Vajana
MaintainerSolange Duruz <[email protected]>
LicenseGPL (>= 2)
Version0.1.2
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("SolangeD/RSambada")
SolangeD/RSambada documentation built on Jan. 8, 2020, 11:21 a.m.