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Formats
Description
Formats for data objects in KinMix and KinMixLite
Formats
An allele frequency database is a data frame containing variables marker, allele and frequency (character, numeric and numeric respectively).
A mixture profile is a data frame containing variables marker, allele and height (character, numeric and numeric respectively).
A genotype profile is a data frame containing variables marker, allele1 and allele2 (character, numeric and numeric respectively).
Examples of these 3 data formats are objects db, epg and Cgt, respectively, in test2data.
A allele count array is an alternative format for a genotype as a named list of vectors, one for each marker. Each vector gives the number of each allele in the genotype, with the alleles listed in the order in which they appear in the data component of the relevant mixture object.
An IBD pattern distribution or IBD object is a list with components pr (a numerical vector) and patt (an integer matrix with nrow(patt)==length(pr) and an even number of columns). The elements of pr are the probabilities of the IBD patterns in the corresponding rows of patt. Adjacent pairs of columns encode the genotypes of different individuals; equal elements in any row determine equality of the alleles; different elements denote independent draws from the gene pool. If the component pr is missing, functions rpt.IBD and rpt.typed.relatives assume the probabilities are equal.
Author(s)
Peter Green (P.J.Green@bristol.ac.uk)