Function reference • SNPfiltR

All functions
`SNPfiltR`	SNPfiltR: A package for interactively visualizing and filtering SNP datasets
`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
`vcfR.example`	Example scrub-jay vcfR file

Reference