ReadHPA: Read Haplotype Presence-Absence (HPA) file

In AdmixPoly: Global and Local Admixture Inference in Polyploids

Read Haplotype Presence-Absence (HPA) file

Description

This function reads and format HPA files generated by HaploCharmer.

Usage

ReadHPA(
  File,
  MaxMarkerMissing = 0.2,
  MaxIndMissing = 0.2,
  TotalDepthField = "DP",
  AlleleDepthField = "AD",
  NbThreads = 0L,
  Verbose = TRUE
)

Arguments

File	Path to HPA file
MaxMarkerMissing	Maximum proportion of missing values for marker above which the marker is discarded
MaxIndMissing	Maximum proportion of missing values for individual above which the individual is discarded (applied after marker filtering)
TotalDepthField	Total read depth FORMAT field in the HPA file to get allele depth proportions
AlleleDepthField	Alternative allele read depth FORMAT field in the HPA file to get allele depth proportions
NbThreads	Number of threads to be used (positive integer) with a default value of 0 setting automatically all threads available
Verbose	A boolean describing if detailed information should be printed

Details

The function ReadHPA() reads Hapotype Presence-Absence (HPA) files generated by HaploCharmer.

This function generates genotypic data coded as haplotype read depth ratios using the read depths from the haplotype (AlleleDepthField) and total read depth (TotalDepthField) fields of the HPA file.

Filtering of missing data can be applied to individuals and markers by setting the maximum percentages MaxMarkerMissing and MaxIndMissing, respectively.

By default, all available threads/CPU cores are used but the number can be chosen using NbThreads.

Value

A list of three items: a filtered list of genotying matrices (Geno), a dataframe with variant information (MarkerInfo), and a dataframe to be used as a genetic map proxy for local admixture inference (GeneticMap). The genetic map proxy is based on physical positions assuming all chromosomes are 100cM long.

See Also

ReadHPA() to read VCF files

Examples

## Read HPA
hpa_path <- system.file("extdata", "Test.hpa", package = "AdmixPoly")
DataHPA <- AdmixPoly::ReadHPA(File = hpa_path, NbThreads=1)

AdmixPoly documentation built on June 18, 2026, 1:06 a.m.