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 27 Oct. 2026.
Previous versions and publish date:
(2026-07-09 06:43), 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

usemodels  
Boilerplate Code for 'Tidymodels' Analyses
Code snippets to fit models using the tidymodels framework can be easily created for a given data se ...
Download / Learn more Package Citations See dependency  
exams2learnr  
Interface for 'exams' Exercises in 'learnr' Tutorials
Automatic generation of quizzes or individual questions for 'learnr' tutorials based on 'R/exams' ex ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
spanish  
Translate Quantities from Strings to Integer and Back. Misc Functions on Spanish Data
Character vector to numerical translation in Euros from Spanish spelled monetary quantities. Reverse ...
Download / Learn more Package Citations See dependency  
SGB  
Simplicial Generalized Beta Regression
Main properties and regression procedures using a generalization of the Dirichlet distribution calle ...
Download / Learn more Package Citations See dependency  

29,218

R Packages

247,686

Dependencies

77,281

Author Associations

29,219

Publication Badges

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