Function reference • MIPanalyzer

All functions
`MIPanalyzer` `MIPanalyzer-package`	MIPanalyzer
`Pf_chrom_lengths()`	Get dataframe of P.falciparum chromosome lengths
`check_MIPanalyzer_loaded()`	Check that MIPanalyzer package has loaded successfully
`explore_filter_coverage_loci()`	Explore locus coverage prior to filtering
`explore_filter_coverage_samples()`	Explore sample coverage prior to filtering
`filter_counts()`	Filter alleles based on raw counts
`filter_coverage_loci()`	Filter loci based on coverage
`filter_coverage_samples()`	Filter samples based on coverage
`filter_loci()`	Filter out some loci
`filter_loci_invariant()`	Filter loci to drop invariant sites
`filter_overcounts()`	Filter out over-counts
`filter_samples()`	Filter out some samples
`filter_wsaf()`	Filter alleles based on within-sample allele frequencies
`get_IBS_distance()`	Get identity by state (IBS) distance
`get_IB_mixture()`	Get identity by mixture
`get_genomic_distance()`	Get genomic distance between samples
`get_spatial_distance()`	Get great circle distance between spatial points
`get_wsaf()`	Get within-sample allele frequencies
`inbreeding_mle()`	Estimate pairwise inbreeding coefficient F by maximum likelihood
`is.mipanalyzer_biallelic()`	Determine if object is of class mipanalyzer_biallelic
`is.mipanalyzer_multiallelic()`	Determine if object is of class mipanalyzer_multiallelic
`lonlat_to_bearing()`	Calculate great circle distance and bearing between coordinates
`mipanalyzer_biallelic_to_vcfR()`	Converts a MIPanalyzer biallelic object to vcfR
`mipanalyzer_file()`	Load system file
`pca_wsaf()`	PCA of within-sample allele frequencies
`pcoa_genomic_distance()`	PCoA of genomic distances between samples
`plot_coverage()`	Plot coverage matrix
`plot_distance()`	Plot a distance matrix
`plot_map()`	Produce ggplot map
`plot_pca()`	Plot PCA
`plot_pca_contribution()`	Plot PCA contribution of each variable
`plot_pca_variance()`	Plot variance explained by PCA components
`plot_pcoa()`	Plot PCoA
`plot_wsaf()`	Plot within-sample allele frequencies
`print(<mipanalyzer_biallelic>)`	Custom print function for class mipanalyzer_biallelic
`print(<mipanalyzer_multiallelic>)`	Custom print function for class mipanalyzer_multiallelic
`rbetabinom()`	Draw from Beta-binomial distribution
`rdirichlet()`	Draw from Dirichlet distribution
`sim_biallelic()`	Simulate biallelic data
`summary(<mipanalyzer_biallelic>)`	Print summary for class mipanalyzer_biallelic
`summary(<mipanalyzer_multiallelic>)`	Print summary for class mipanalyzer_multiallelic
`vcf_to_mipanalyzer_biallelic()`	Convert vcf to biallelic mipanalyzer data class
`vcf_to_mipanalyzer_multiallelic()`	Convert vcf to multiallelic mipanalyzer data class

Reference

All functions