R.SamBada: 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).
| Version: |
0.1.3 |
| 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: |
2022-01-05 |
| 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 |
Documentation:
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