Relationship-Informed Pedigree and Variant Scoring

Documentation for package ‘KinformR’ version 0.1.2

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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.