editraw {hsrecombi}

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)