phcp_impute: Imputation for pseudo-haplotypes
In ShamamW/PHCPImpute: PHCP-BASED IMPUTATION

phcp_impute

R Documentation

Imputation for pseudo-haplotypes

Description

This function perform imputation of pseudo-haplotypes. The imputation is based on Lee and Li & Stephens hidden Markov model, as implemented in ChromoPainter, but with the hidden state representing a pair of haplotypes from the reference panel.

Usage

phcp_impute(
  haps,
  ancient_tped,
  genetic_map,
  chr,
  choose_donors = F,
  freq_donors = 0.5,
  variants
)

Arguments

`haps`	a data frame of Phased reference genomes in .haps format, which is the output of SHAPEIT2.
`ancient_tped`	a data frame of pseudo-haplotype to impute in Plink tped format.
`genetic_map`	a data frame of genetic map for the reference genome with 3 columns: chromosome number, genetic distance in Morgans, physical position. The columns header should be: chr, genetic_distance, bp
`chr`	the number of chromosome to impute (integer).
`choose_donors`	the number of haplotypes to choose from the reference data for the imputation. If FALSE, all haplotypes in the data will be used.
`freq_donors`	the maximal minor allele frequency in variants to consider when choosing the donors
`variants`	a data frame with variants to impute . If the arguments is missing, all variants of the reference panel will be be imputed.

Value

A data frames with the posterior probabilities of the possible genotypes in the imputed variants.

References

N. Li, M. Stephens, Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165, 2213-2233 (2003)

D. J. Lawson, G. Hellenthal, S. Myers, D. Falush, Inference of population structure using dense haplotype data. PLoS Genet 8, e1002453 (2012)

ShamamW/PHCPImpute documentation built on Oct. 26, 2022, 6:34 a.m.