ped
a data frame in ped format, i.e. the first six columns must contain information on the families as typically
presenteed in ped files, where
the column names of these six columns must be "famid", "pid", "fatid", "motid", "sex","affected". The last two
of these six columns are ignored. The IDs of individuals in the second column must be unique (not only within the family,
but among all individuals). The columns following the six columns are assumed to contain the alleles of the SNPs, where
the alleles are coded using the letters/numbers in coded, and missing values are coded by naVal. Thus, the
seventh and the eigth column contain the two alleles for the first SNP, the ninth and tenth the two alleles for the second
SNP, and so on. Contrary to the names of the first six columns, the names of the columns representing the SNPs are ignored,
and SNP names can be specified using snpnames.
snpnames
a character vector containing the names of the SNPs. If not specified, generic names are assigned (i.e.
SNP1, SNP2, ...). Ignored if ped just contains one SNPs.
coded
the coding used for the alleles of the SNPs. coded = "12", e.g., means that one of the alleles is coded
by 1, and the other by 0. coded = "ATCG" means that the alleles are coded by the actual base.