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

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 < https://github.com/Sylvie/sambada>. 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).


News

R.SamBada 0.1.1

Bug fixes

  • downloadSambada: bug fix for MacOS
  • prepareGeno, sambadaParallel: error message when sambada is not installed
  • plotResultInteractive: bug fix when click on Manhattan plot

Update of the vignette and documentation

  • Simplification of the vignette. Some details have been moved from the vignette to the documentation. Reference to files used in the vignette is simplified.

Updates in the test dataset

  • Update of the file 'uganda-subset-mol-Out-2.csv'

Reference manual

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install.packages("R.SamBada")

0.1.1 by Solange Duruz, 4 months ago


Browse source code at https://github.com/cran/R.SamBada


Authors: Solange Duruz , Sylvie Stucki , Oliver Selmoni , Elia Vajana


Documentation:   PDF Manual  


GPL (>= 2) license


Imports SNPRelate, gdsfmt

Suggests Rcpp, utils, data.table, shiny, plotly, httr, biomaRt, ggplot2, sp, packcircles, raster, mapplots, spdep, rgdal, gdalUtils, rworldmap, doParallel, foreach, knitr, rmarkdown


See at CRAN