R.SamBada

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) <doi:10.1111/1755-0998.12629> 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).

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Description file content

Package
R.SamBada
Type
Package
Title
Processing Pipeline for 'SamBada' from Pre- To Post-Processing
Version
0.1.1
Date
2019-05-07
Author
Solange Duruz, Sylvie Stucki, Oliver Selmoni, Elia Vajana
Maintainer
Solange Duruz
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).
License
GPL (>= 2)
Imports
SNPRelate, gdsfmt
LinkingTo
RoxygenNote
6.1.0
Suggests
Rcpp, utils, data.table, shiny, plotly, httr, biomaRt, ggplot2, sp, packcircles, raster, mapplots, spdep, rgdal, gdalUtils, rworldmap, doParallel, foreach, knitr, rmarkdown
VignetteBuilder
knitr
NeedsCompilation
no
Packaged
2019-05-09 10:11:08 UTC; Solange
Repository
CRAN
Date/Publication
2019-05-09 10:50:02 UTC

install.packages('R.SamBada')

0.1.1

2 months ago

Solange Duruz

GPL (>= 2)

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

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