Internal function for converting an R matrix object into the new format of data used in Haplin. The output is the same as from genDataRead.
f.convert.matrix.ff(
data = stop("You must give the data to convert!", call. = FALSE),
n.vars = stop("You must explicitly give the number of columns with covariates!", call.
= FALSE),
cov.header,
gen.levels
)A list object with two elements:
cov.data - a data.frame with covariate data (if available in
the input file)
gen.data - a list with chunks of the genetic data; the data is divided column-wise, using 10,000 columns per chunk; each element of this list is a ff matrix
A character matrix (NB: it's assumed that this matrix contains genotypes and covariate data, if any; i.e., as if it was a table read in from a haplin-formatted file).
Number of columns with covariate variables - if the data does not contain covariates, give 0 explicitly.
Optional; if there are covariates in the data, you can give their names explicitly here. Otherwise, dummy names will be created.
Optional; a vector with all the possible values for alleles in the genotype part of data. If not given, these will be assessed from the given data.