The R.SamBada package provides functions that can be classified into four categories: Install samBada, Preprocessing, Running samBada and Post-processing.
You can download samBada (if not already on your computer) from GitHub using the function downloadSambada
The Preprocessing functions contain three functions:
prepareGeno: translate genomic file to samBada's input file while applying genomic filters
setLocation: opens local web page with interactive map to assign sample location
createEnv: create your environmental file from file location from local raster or global worldclim database
prepareEnv: reduce environmental file with correlated variables and analyse population structure
To run samBada, you will want to use the function: sambadaParallel
The Postprocessing functions contain three functions:
prepareOutput: calculate p and q-values from samBada output and retrieve SNP position for manhattan plots
plotManhattan: create a manhattan plot of one or several environmental variables
plotResultInteractive: start an interactive local web page to query a manhattan plot with maps, plots and ensembl query result
plotMap: create a map of marker, population structure or environmental variable distribution