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R.SamBada (version 0.1.3)

Processing Pipeline for 'SamBada' from Pre- To Post-Processing

Description

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) and . 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).

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Version

Install

install.packages('R.SamBada')

Monthly Downloads

55

Version

0.1.3

License

GPL (>= 2)

Maintainer

Solange Duruz

Last Published

January 5th, 2022

Functions in R.SamBada (0.1.3)

downloadSambada

Download samBada
prepareEnv

Prepare environmental input
plotManhattan

Manhattan plot
prepareGeno

Prepare genomic input
setLocation

Set the location of samples through a local web-application with interactive map
prepareOutput

Prepare output (useful for all postprocessing analysis)
sambadaParallel

Run sambada on parallel cores
R.SamBada-package

R.SamBada: A package for running samBada within R with pipeline from pre to post-processing
createEnv

Create env file from raster file(s) and/or global database present in the raster r package
plotMap

Plotting of maps
plotResultInteractive

Interactive plotting of results