R.SamBada-package: R.SamBada: A package for running samBada within R with...

In R.SamBada: Processing Pipeline for 'SamBada' from Pre- To Post-Processing

Description

The R.SamBada package provides functions that can be classified into four categories: 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 environmental 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 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

R.SamBada documentation built on Jan. 5, 2022, 1:08 a.m.