CRAN/E | SNPfiltR

SNPfiltR

Interactively Filter SNP Datasets

Installation

About

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.

Key Metrics

Version 1.0.1
R ≥ 2.10
Published 2023-03-17 454 days ago
Needs compilation? no
License MIT
License File
CRAN checks SNPfiltR results

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Maintainer

Maintainer

Devon DeRaad

Authors

Devon DeRaad

aut / cre

Material

README
Reference manual
Package source

Vignettes

reproducible-vignette

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

SNPfiltR archive

Depends

R ≥ 2.10

Imports

vcfR
ggplot2
Rtsne
cluster
adegenet
gridExtra
ggridges
stats
graphics
utils

Suggests

rmarkdown
knitr