geneticPosition | R Documentation |
Estimation of genetic positions (in centi Morgan)
geneticPosition(final, map1, exclude = NULL, threshold = 0.05)
final |
table of results produced by |
map1 |
data.frame containing information on physical map, at least:
|
exclude |
optional vector (LEN < p) of SNP IDs to be excluded (e.g., candidates of misplaced SNPs; default NULL) |
threshold |
optional value; recombination rates <= threshold are considered for smoothing approach assuming theta ~ Morgan (default 0.05) |
Smoothing of recombination rates (theta) <= 0.05 via quadratic optimization provides an approximation of genetic distances (in Morgan) between SNPs. The cumulative sum * 100 yields the genetic positions in cM.
The minimization problem (theta - D d)^2
is solved s.t. d > 0 where
d is the vector of genetic distances between adjacent markers but theta is
not restricted to adjacent markers. The incidence matrix D contains 1's for
those intervals contributing to the total distance relevant for each theta.
Estimates of theta = 1e-6 are neglected as these values coincide with start values and indicate that (because of a very flat likelihood surface) no meaningful estimate of recombination rate has been obtained.
list (LEN 2)
vector (LEN p) of genetic positions of SNPs (in cM)
vector (LEN p) of physical positions of SNPs (in Mbp)
Qanbari, S. & Wittenburg, D. (2020) Male recombination map of the autosomal genome in German Holstein. Genetics Selection Evolution 52:73. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/s12711-020-00593-z")}
### 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)
### approximation of genetic positions
pos <- geneticPosition(final, map.chr)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.