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) <10.1111> 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).10.1111>
- downloadSambada: bug fix for MacOS
- prepareGeno, sambadaParallel: error message when sambada is not installed
- plotResultInteractive: bug fix when click on Manhattan plot
Update of the vignette and documentation
- Simplification of the vignette. Some details have been moved from the vignette to the documentation. Reference to files used in the vignette is simplified.
Updates in the test dataset
- Update of the file 'uganda-subset-mol-Out-2.csv'