R: Interactively Filter SNP Datasets

# Interactively Filter SNP Datasets

## Documentation for package ‘SNPfiltR’ version 1.0.7

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

assess_missing_data_pca | Vizualise how missing data thresholds affect sample clustering
assess_missing_data_tsne | Vizualise how missing data thresholds affect sample clustering
distance_thin | Filter a vcf file based on distance between SNPs on a given scaffold
filter_allele_balance | Filter out heterozygous genotypes failing an allele balance check
filter_biallelic | Remove SNPs with more than two alleles
hard_filter | Hard filter a vcf file by depth and genotype quality (gq)
max_depth | Vizualise and filter based on mean depth across all called SNPs
min_mac | Vizualise, filter based on Minor Allele Count (MAC)
missing_by_sample | Vizualise missing data per sample, remove samples above a missing data cutoff
missing_by_snp | Vizualise missing data per SNP, remove SNPs above a missing data cutoff
popmap | Popmap for example scrub-jay vcfR file
SNPfiltR | SNPfiltR: A package for interactively visualizing and filtering SNP datasets
vcfR.example | Example scrub-jay vcfR file