create.pairs.frame {ibdreg} | R Documentation |
create a data frame for relative pairs containing identifiers, response, and covariates
create.pairs.frame(ibd.dat, model.mat, formula, c.scale) create.pairs.frame.cvec(c.scale, prior2, prior1)
ibd.dat |
object of class ibd.dat |
model.mat |
a model matrix containing covariates for each person; to be used in making covariates for the relative pair |
formula |
format is either ~1 or ~pairs.fun(cov1). If the latter, the columns of the returned x.mat will be the result of the function operated on the covariate for each relative in the relative pair. |
c.scale |
scaling factor for covariates. Either "nodom" for no dominance variance or "minimax". |
prior2 |
Prior probability of relative pairs to share 2 alleles ibd (from ibd.dat object) |
prior1 |
Prior probability of relative pairs to share 1 allele ibd (from ibd.dat object) |
a list of 3 data frames all with the same number of rows. These data frames are id.df (3-columns of ped.id, person1.id, person2.id), y.mat (estimated ibd allele sharing, which is the regression response), status.df (3-columns for AA, UU, or AU status for the pair), x.mat (model matrix with intercept and, if covariates in formula, columns for covariates).