R/RSamBada.R

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

#' R.SamBada: A package for running samBada within R with pipeline from pre to post-processing
#'
#' The R.SamBada package provides functions that can be classified into four categories:
#' Install samBada, Preprocessing, Running samBada and Post-processing.
#' 
#' @section Install samBada functions:
#' You can download samBada (if not already on your computer) from GitHub using the function \code{\link{downloadSambada}}
#' 
#' @section Preprocessing functions:
#' The Preprocessing functions contain three functions: 
#'\itemize{
#'\item{\code{\link{prepareGeno}}: translate genomic file to samBada's input file while applying genomic filters}  
#'\item{\code{\link{setLocation}}: opens local web page with interactive map to assign sample location}  
#'\item{\code{\link{createEnv}}: create your environmental file from file location from local raster or global worldclim database}
#'\item{\code{\link{prepareEnv}}: reduce environmental file with correlated variables and analyse population structure}
#'}
#' 
#' @section Running samBada function:
#' To run samBada, you will want to use the function: \code{\link{sambadaParallel}}
#' 
#' @section Postprocessing functions:
#' The Postprocessing functions contain three functions: 
#'\itemize{
#'\item{\code{\link{prepareOutput}}: calculate p and q-values from samBada output and retrieve SNP position for manhattan plots}
#'\item{\code{\link{plotManhattan}}: create a manhattan plot of one or several environmental variables}
#'\item{\code{\link{plotResultInteractive}}: start an interactive local web page to query a manhattan plot with maps, plots and ensembl query result}
#'\item{\code{\link{plotMap}}: create a map of marker, population structure or environmental variable distribution}
#'}
#'
#' @importFrom grDevices colorRampPalette colors dev.off dev.size pdf png terrain.colors
#' @importFrom graphics abline axis barplot boxplot hist image layout lines par plot plot.new points text
#' @importFrom stats aggregate complete.cases cor cutree hclust kmeans na.exclude pchisq splinefun
#' @importFrom utils data read.csv read.table write.table
#'
#' @docType package
#' @name R.SamBada-package
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