editraw: Editing results of hsrecombi
In hsrecombi: Estimation of Recombination Rate and Maternal LD in Half-Sibs

editraw

R Documentation

Editing results of hsrecombi

Description

Process raw results from hsrecombi, decide which out of two sets of estimates is more likely and prepare list of final results

Usage

editraw(Roh, map1)

Arguments

Roh

list of raw results from hsrecombi

map1

data.frame containing information on physical map, at least:

SNP: SNP ID
locus_Mb: physical position in Mbp of SNP on chromosomes
Chr: chromosome of SNP

Value

final table of results

SNP1: index 1. SNP
SNP2: index 2. SNP
D: maternal LD
fAA: frequency of maternal haplotype 1-1
fAB: frequency of maternal haplotype 1-0
fBA: frequency of maternal haplotype 0-1
fBB: frequency of maternal haplotype 0-0
p1: Maternal allele frequency (allele 1) at SNP1
p2: Maternal allele frequency (allele 1) at SNP2
nfam1: size of genomic family 1
nfam2: size of genomic family 2
error: 0 if computations were without error; 1 if EM algorithm did not converge
iteration: number of EM iterations
theta: paternal recombination rate
r2: r^2 of maternal LD
logL: value of log likelihood function
unimodal: 1 if likelihood is unimodal; 0 if likelihood is bimodal
critical: 0 if parameter estimates were unique; 1 if parameter estimates were obtained via decision process
locus_Mb: physical distance between SNPs in Mbp

Examples

  ### test data
  data(targetregion)
  ### make list for paternal half-sib families
  hap <- makehaplist(daughterSire, hapSire)
  ### parameter estimates on a chromosome
  res <- hsrecombi(hap, genotype.chr)
  ### post-processing to achieve final and valid set of estimates
  final <- editraw(res, map.chr)

hsrecombi documentation built on June 7, 2023, 6:02 p.m.