vcfR.example

<p>A vcfR object containing 500 SNPs for 20 individuals. Species assignments for
each individual can be accessed via SNPfiltR::popmap</p>

datasets

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.

Devon DeRaad

SNPfiltR

Interactively Filter SNP Datasets

vcfR.example function

<p>A vcfR object containing 500 SNPs for 20 individuals</p>

vcfR.example: Example scrub-jay vcfR file

Description

Usage

Arguments

Format