Package: SNPfiltR
Title: Interactively Filter SNP Datasets
Version: 1.0.7
Authors@R: person(given = "Devon",
           family = "DeRaad",
           role = c("aut", "cre"),
           email = "devonderaad@gmail.com",
           comment = c(ORCID = "0000-0003-3105-985X"))
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' authored by Knaus and Grünwald (2017) <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.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Imports: vcfR, ggplot2, Rtsne, cluster, adegenet, gridExtra, ggridges,
        stats, graphics, utils
Depends: R (>= 2.10)
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-09-03 17:55:21 UTC; devder
Author: Devon DeRaad [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3105-985X>)
Maintainer: Devon DeRaad <devonderaad@gmail.com>
Repository: CRAN
Date/Publication: 2025-09-04 06:40:39 UTC
Built: R 4.6.0; ; 2026-04-26 15:14:14 UTC; unix
