checkCandidates {hsrecombi}

Candidates for misplacement

Description

Search for SNPs with unusually large estimates of recombination rate

Usage

checkCandidates(final, map1, win = 30, quant = 0.99)

Arguments

final

table of results produced by editraw with pairwise estimates of recombination rate between p SNPs within chromosome; minimum required data frame with columns SNP1, SNP2 and theta

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

win

optional value for window size; default value 30

quant

optional value; default value 0.99, see details

Details

Markers with unusually large estimates of recombination rate to close SNPs are candidates for misplacement in the underlying assembly. The mean of recombination rate estimates with win subsequent or preceding markers is calculated and those SNPs with mean value exceeding the quant quantile are denoted as candidates which have to be manually curated! This can be done, for instance, by visual inspection of a correlation plot containing estimates of recombination rate in a selected region.

Value

vector of SNP IDs for further verification

References

Hampel, A., Teuscher, F., Gomez-Raya, L., Doschoris, M. & Wittenburg, D. (2018) Estimation of recombination rate and maternal linkage disequilibrium in half-sibs. Frontiers in Genetics 9:186. doi: 10.3389/fgene.2018.00186

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)
  ### check for candidates of misplacement
  snp <- checkCandidates(final, map.chr)