phase_donor_haplotypes: A function to drive the phasing and reporting of the two...

In mccoy-lab/rhapsodi: R haploid sperm/oocyte data imputation

A function to drive the phasing and reporting of the two haplotypes from a single diploid donor

Description

This function infers the diploid donor haplotypes by first calling split_with_overlap to construct the overlapping SNP segments, then reconstruct_hap for majority voting within each overlapping segment, finally stitching together the overlapping segments to phase both haplotypes using stitch_haplotypes

Usage

phase_donor_haplotypes(
  dt,
  positions,
  window_length = 3000,
  overlap_denom = 2,
  threads = 2,
  mcstop = TRUE,
  stringent_stitch = TRUE,
  stitch_new_min = 0.5,
  calculate_window_size_bool = FALSE,
  cov = NULL,
  ger = NULL,
  avgr = NULL
)

Arguments

dt	Matrix or dataframe of gamete alleles in 0/1/NA encoding
positions	vector of SNP positions
window_length	An integer; size of window for split_with_overlap (default=3000)
overlap_denom	An integer; value for denominator in calculation of overlap for split_with_overlap (default = 2)
threads	An integer; Number of threads to use when calling pbmclapply or the like (default = 2)
mcstop	A bool; whether to stop phasing if mean_concordance isn't within advised bounds during stitching in stitch_haplotypes (default = TRUE ). TRUE stops phasing, FALSE allows it to continue, finding the minimum linear distance between the concordance and the thresholds.
stringent_stitch	A bool; whether or not to use the original bounds (0.1, 0.9 cutoff) in stitch_haplotypes, or a user specified threshold value stitch_new_min.
stitch_new_min	A numeric/float, if stringent_stitch == FALSE, the new minimum value to use as a cutoff in stitch_haplotypes. If concordance is below this value, we assume the windows are opposite haplotypes, if greater than or equal, we assume the same haplotypes
calculate_window_size_bool	A bool; whether or not to calculate the window size based on characteristics of the input dataset; default = FALSE
cov	A numeric; the expected sequencing depth coverage, necessary only if wanting rhapsodi to calculate the preferred window size; default = NULL
ger	A numeric; the expected genotyping error rate, necessary only if wanting rhapsodi to calculate the preferred window size; default = NULL
avgr	A numeric; the expected average recombination rate, necessary only if wanting rhapsodi to calculate the preferred window size; default = NULL

Value

complete_haplotypes phased haplotypes as a data frame with column names index, pos (for SNP positions), h1 (haplotype 1), & h2 (haplotype 2)

mccoy-lab/rhapsodi documentation built on July 27, 2022, 3:56 a.m.