monotone_regression {gpmap} | R Documentation |
Perform monotone regression on a genotype-phenotype (GP) map
Description
The function uses partial_genotype_order
and activeSet
from the isotone package to do
monotone regression (Leeuw et al., 2009) on a GP map.
Usage
monotone_regression(gpmap, plusallele)
Arguments
gpmap |
An object of class |
plusallele |
An |
Details
Element i in plusallele
specifies the ordering of the genotypes at locus i, if the element is 1 then 11 < 12 < 22 and conversely if it is 2 then
22 < 12 < 11. monotone_regression
calls partial_genotype_order
to obtain the partial ordering of genotypic values for the given plusalleles
.
This partial ordering is then used together with the GP map itself as input to the activeSet
function from the package
isotone.
Value
monotone_regression
returns the output from activeSet
directly.
Author(s)
Arne B. Gjuvsland <arne.gjuvsland@nmbu.no> and Yunpeng Wang <yunpeng.wng@gmail.com>
References
Leeuw J, Hornik K and Mair P (2009) Isotone Optimization in R: Pool-Adjacent-Violators Algorithm (PAVA) and Active Set Methods. Journal of Statistical Software 32(5) [link]
Gjuvsland AB, Wang Y, Plahte E and Omholt SW (2013) Monotonicity is a key feature of genotype-phenotype maps. Front. Genet. 4:216. doi: 10.3389/fgene.2013.00216 [link]
Examples
data(GPmaps)
#Additive GP map is monotone
monotone_regression(A,c(2,2))
#Pure AxA epistasis map
monotone_regression(AA,c(2,2))
#two-locus example in Cheverud & Routman (1995)
monotone_regression(mouseweight,c(1,1))