RSambada-package: RSambada: A package for running sambada within R with...

In SolangeD/sambadaOnR: Processing Pipeline for 'SamBada' from Pre- To Post-Processing

Description

The RSambada package provides four categories of important functions: Install sambada, Preprocessing, Running sambada and Post-processing.

Install sambada functions

You can download sambada (if not already on your computer) from GitHub using the function downloadSambada

Preprocessing functions

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

Running sambada function

To run sambada, you will want to use the function: sambadaParallel

Postprocessing functions

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

SolangeD/sambadaOnR documentation built on Dec. 25, 2021, 12:19 a.m.