add.fam.scores          Sum all the given scores and return a single
                        vector with cumulative "score", "for" and
                        "against" vals. For use in instances where one
                        wishes to combine scores from multiple
                        families.
assign.a                For affecteds: Take genetic variant and
                        determine the category of the combo.
assign.status           Take a disease status and a genetic variant and
                        determine which category the combo falls in.
                        A.c = Affected individual with ALT variant A.i
                        = Affected individual without ALT variant U.c =
                        Unaffected individual without ALT variant U.i =
                        Unaffected individual with ALT variant If
                        theoretical.max = TRUE the true variant
                        statuses are ignored and all
                        affected/unaffected are assigned A.c and U.c
                        respectively. These encoding can then be used
                        show what a family's max score would be.
assign.u                For unaffecteds: Take a genetic variant and
                        determine the category of the combo.
build.relation.dict     Build dictionary with the relationships falling
                        in the different categories for the query row.
calc.rv.score           Calculate a relatedness-weighted score for a
                        given rare variant.
encode.rows             Take the relationship matrix and the encoded
                        statuses of info. For each row, generate the
                        encoded data for scoring.
ibd                     Calculation of Identity by descent (IBD).
penetrance              Likelihood function for calculation of
                        Pedigree-based autosomal dominant penetrance
                        value. Formula deployed via optimize so as to
                        determine the optimal value.
read.indiv              Read in variant and status info for
                        individuals.
read.pedigree           Read in the encoded pedigree data file.
read.relation.mat       Read in relationship matrix Apply the
                        individual names to the rows and columns.
read.var.table          Read in a vcf-like subset of information
                        obtained from use of seqbiopy's vcf_extract
                        function on a vcf with the status encoded in
                        the indivudal's names
score                   Score the pedigrees using the pihat values.
score.fam               Given a relationship matrix and status
                        dataframe, score a family by applying the
                        calc.rv.score scoring system to every pairwise
                        combination of individuals.
score.pedigree          Take the encoded information about the
                        pedigrees and calculate penetrance.
score.variant.status    Take the dataframe with variants and status and
                        determine which indivudals are scored correctly
                        and which are scored incorrectly. Assign an
                        A.c, A.i, U.c, U.i, unk
subset.mat              Take the matrix and subset out only the encoded
                        individuals that are present in the status
                        dataframe.
