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prewas
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]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-02-25
Latest Update: 2023-03-21
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
Previous versions and publish date:
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imports, suggests or enhances
Functions, R codes and Examples using
the prewas R package
Some associated functions: collapse_snps_into_genes . collapse_snps_into_genes_by_impact . gff . outgroup . prewas . results . snpeff_vcf . tree . vcf .
Some associated R codes: collapse_snps_by_gene.R . data.R . dup_snps_in_overlapping_genes.R . format_inputs.R . generate_allele_matrix.R . preprocess_tree_and_vcf.R . prewas.R . reference_alleles.R . split_multiallelic_snps.R . validate.R . Full prewas package functions and examples
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