The RSambada package provides four categories of important functions: Install sambada, Preprocessing, Running sambada and Post-processing.
You can download sambada (if not already on your computer) from GitHub using the function
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 envrionmental file with correlated variables and analyse population structure
To run sambada, you will want to use the function:
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 envrionmental 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
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