editraw: Editing results of hsrecombi

Description Usage Arguments Value Examples

View source: R/functions.R

Description

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

Usage

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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) SNP1

p2

Maternal allele frequency (allele 1) 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

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  ### 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, map.chr$SNP)
  ### post-processing to achieve final and valid set of estimates
  final <- editraw(res, map.chr)

hsrecombi documentation built on March 23, 2021, 9:07 a.m.