Interactively Filter SNP Datasets

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Documentation for package ‘SNPfiltR’ version 1.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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