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).
| Version: | 0.1.2 |
| Imports: | SNPRelate, gdsfmt |
| Suggests: | Rcpp, utils, data.table, shiny, plotly, httr, biomaRt, ggplot2, sp, packcircles, raster, mapplots, spdep, rgdal, gdalUtils, rworldmap, doParallel, foreach, knitr, rmarkdown |
| Published: | 2019-11-25 |
| Author: | Solange Duruz, Sylvie Stucki, Oliver Selmoni, Elia Vajana |
| Maintainer: | Solange Duruz <solange.duruz at alumni.epfl.ch> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | no |
| Materials: | NEWS |
| CRAN checks: | R.SamBada results |
| Reference manual: | R.SamBada.pdf |
| Vignettes: |
R.SamBada |
| Package source: | R.SamBada_0.1.2.tar.gz |
| Windows binaries: | r-devel: R.SamBada_0.1.2.zip, r-release: R.SamBada_0.1.2.zip, r-oldrel: R.SamBada_0.1.2.zip |
| macOS binaries: | r-release: R.SamBada_0.1.2.tgz, r-oldrel: R.SamBada_0.1.2.tgz |
| Old sources: | R.SamBada archive |
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