R: Relationship-Informed Pedigree and Variant Scoring

# Relationship-Informed Pedigree and Variant Scoring

## Documentation for package ‘KinformR’ version 0.1.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

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.