Package index • PGEcore

Getting started helpers

Lightweight summaries and COI utilities with no specialised Suggests.

count_samples_by_coi(): Count specimens by complexity of infection (COI)
estimate_coi_naive(): Estimate COI using naive allele-count methods
estimate_allele_frequency_naive(): Estimate allele frequency naively from AA or microhaplotype calls
estimate_allele_prevalence_naive(): Estimate allele prevalence naively from AA or microhaplotype calls
allele_per_locus_summary(): Summarize alleles per locus from an allele table

filter_biallelic_calls(): Filter amino acid calls to biallelic loci
filter_to_highest_diversity_independent_snp_call(): Filter SNPs to highest-diversity loci spaced by a minimum distance
slaf_from_mhaps_freqs(): Calculate single-locus allele frequencies from microhaplotype frequencies
slaf_from_stave_mlaf(): Convert STAVE multi-locus allele frequencies to single-locus frequencies
convert_single_locus_table_to_stave(): Convert a single-locus table to STAVE-style variant identifiers
multilocus_prevfreq_naive(): Estimate multilocus prevalence and frequency with naive phasing
multilocus_prevfreq_naive_variantstring(): Estimate multilocus prevalence and frequency with variantstring
snp_calls_to_vcf(): Build a VCF from pileup SNP calls
vcf_to_snp_calls(): Convert a VCF with FORMAT/AD into pileup-style SNP calls
add_ref_seqs_with_targeted_ref_fasta(): Add reference sequences from a targeted FASTA onto a panel BED table
add_ref_seqs_with_full_genome_ref_fasta(): Add reference sequences extracted from a genome FASTA onto a panel BED table

Require Biostrings and related Suggests (and often MSA binaries on PATH).

pileup_specific_snps(): Pile up specific SNPs covered by microhaplotype sequences
translate_loci_of_interest(): Translate loci of interest from microhaplotype sequences
per_locus_popgen_summary(): Per-locus nucleotide diversity, segregating sites, and Tajima's D

Optional packages must be installed separately (see README Suggests table). Prefer these file/CLI entry points.

coiaf_wrapper(): Estimate COI with coiaf from SNP-call and output paths
dcifer_slaf_wrapper(): Estimate single-locus allele frequencies with Dcifer
dcifer_ibd_wrapper(): Estimate IBD-based relatedness with Dcifer
moire_wrapper(): Run MOIRE from allele-table and output paths
malariaem_wrapper(): Run malaria.em from allele-table and output paths
snpslice_wrapper(): Estimate multilocus allele frequency and COI with SNP-Slice
FreqEstimationModel_wrapper(): Estimate multilocus allele frequencies with FreqEstimationModel
calculate_fws_from_vcf(): Calculate within-host Fws from a VCF via moimix
IDM_wrapper(): Estimate single-locus allele frequencies with the Incomplete Data Model
MultiLociBiallelicModel_wrapper(): Estimate multilocus haplotype frequencies with MultiLociBiallelicModel
THEREALMcCOIL_wrapper(): Estimate COI and allele frequencies with THEREALMcCOIL

Optional run_* APIs for a few wrappers when data are already in R.