Other packages > Find by keyword >

prewas  

Data Pre-Processing for Bacterial Genome-Wide Association Studies
View on CRAN: Click here


Download and install prewas package within the R console
Install from CRAN:
install.packages("prewas")

Install from Github:
library("remotes")
install_github("cran/prewas")

Install by package version:
library("remotes")
install_version("prewas", "1.1.1")



Attach the package and use:
library("prewas")
Maintained by
Katie Saund
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-02-25
Latest Update:
Description:
Standardize the pre-processing of genomic variants beforeperforming a bacterial genome-wide association study bGWAS. prewascreates a variant matrix where each row is a variant each column is asample and the entries are presence - 1 - or absence - 0 - of the variantthat can be used as input for bGWAS tools. When creating the binary variantmatrix prewas can perform 3 pre-processing steps including dealing withmultiallelic SNPs optional dealing with SNPs in overlapping genes andchoosing a reference allele. prewas can output matrices for use with bothSNP-based bGWAS and gene-based bGWAS. This method is described in Saund etal. 2020 doi10.1099mgen.0.000368. prewas can also providegene matrices for variants with specific annotations from the SnpEffsoftware Cingolani et al. 2012.
How to cite:
Katie Saund (2020). prewas: Data Pre-Processing for Bacterial Genome-Wide Association Studies. R package version 1.1.1, https://cran.r-project.org/web/packages/prewas. Accessed 04 Jun. 2026.
Previous versions and publish date:
1.0.0 (2020-02-25 15:50), 1.1.0 (2020-03-21 18:10), 1.1.1 (2021-04-02 14:20)
Other packages that cited prewas R package
View prewas citation profile
Other R packages that prewas depends, imports, suggests or enhances
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

murphydiagram  
Murphy Diagrams for Forecast Comparisons
Data and code for the paper by Ehm, Gneiting, Jordan and Krueger ('Of Quantiles and Expectiles: Con ...
Download / Learn more Package Citations See dependency  
phers  
Calculate Phenotype Risk Scores
Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and ...
Download / Learn more Package Citations See dependency  
crplyr  
A 'dplyr' Interface for Crunch
In order to facilitate analysis of datasets hosted on the Crunch data platform ...
Download / Learn more Package Citations See dependency  
AMPLE  
Shiny Apps to Support Capacity Building on Harvest Control Rules
Three Shiny apps are provided that introduce Harvest Control Rules (HCR) for fisheries management. ...
Download / Learn more Package Citations See dependency  
golem  
A Framework for Robust Shiny Applications
An opinionated framework for building a production-ready 'Shiny' application. This package contains ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  

27,268

R Packages

233,548

Dependencies

72,590

Author Associations

27,205

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA