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SNPfiltR
View on CRAN: Click
here
Download and install SNPfiltR package within the R console
Install from CRAN:
install.packages("SNPfiltR")
Install from Github:
library("remotes")
install_github("cran/SNPfiltR")
Install by package version:
library("remotes")
install_version("SNPfiltR", "1.0.1")
Attach the package and use:
library("SNPfiltR")
Maintained by
Devon DeRaad
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-10-28
Latest Update: 2023-03-17
Description:
Is designed to interactively and reproducibly visualize and filter SNP (single-nucleotide polymorphism) datasets. This R-based implementation of SNP and genotype filters facilitates an interactive and iterative SNP filtering pipeline, which can be documented reproducibly via Rmarkdown. 'SNPfiltR' contains functions for visualizing various quality and missing data metrics for a SNP dataset, and then filtering the dataset based on user specified cutoffs. All functions take 'vcfR' objects as input, which can easily be generated by reading standard vcf (variant call format) files into R using the R package 'vcfR' (Knaus and Grünwald) (<doi:10.1111/1755-0998.12549>). Each 'SNPfiltR' function can return a newly filtered vcfR object, which can then be written to a local directory in standard vcf format using the 'vcfR' package, for downstream population genetic and phylogenetic analyses.
How to cite:
Devon DeRaad (2021). SNPfiltR: Interactively Filter SNP Datasets. R package version 1.0.1, https://cran.r-project.org/web/packages/SNPfiltR. Accessed 21 Nov. 2024.
Previous versions and publish date:
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Complete documentation for SNPfiltR
Functions, R codes and Examples using
the SNPfiltR R package
Some associated functions: SNPfiltR . assess_missing_data_pca . assess_missing_data_tsne . distance_thin . filter_allele_balance . filter_biallelic . hard_filter . max_depth . min_mac . missing_by_sample . missing_by_snp . popmap . vcfR.example .
Some associated R codes: SNPfiltR.R . assess_missing_data_pca.R . assess_missing_data_tsne.R . distance_thin.R . example_data.R . filter_allele_balance.R . filter_biallelic.R . hard_filter.R . max_depth.R . min_mac.R . missing_by_sample.R . missing_by_snp.R . zzz.R . Full SNPfiltR package functions and examples
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