checkCandidates | R Documentation |
Search for SNPs with unusually large estimates of recombination rate
checkCandidates(final, map1, win = 30, quant = 0.99)
final |
table of results produced by |
map1 |
data.frame containing information on physical map, at least:
|
win |
optional value for window size; default value 30 |
quant |
optional value; default value 0.99, see 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.
vector of SNP IDs for further verification
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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3389/fgene.2018.00186")}
### 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)
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