new.family: New Family Object

In jweile/maveclin: Clinical predictions for MaveDB

Description

Creates a new family object, allowing for calculation of a Bayes factor. The Bayes Factor Represents the likelyhood ratio of a phenotype being caused by an allele in question.

Usage

new.family(maf, etiologic.fraction, penetrance, self = c("heterozygous",
  "homozygous"), modus = c("dominant", "recessive"))

Arguments

maf	Minor Allele Frequency of allele in question
etiologic.fraction	The fraction of symptomatic patients that carry the genotype
penetrance	The fraction of genotype carriers that are symptomatic
self	The genotype of the patient him/herself. "heterozyogus" or "homozygous"
modus	The mode of inheritance. "dominant" or "recessive"

Details

A family object offers the following functions:

• add.parent(pheno) Adds a parent to the family, with boolean parameter pheno indicating whether the parent has the phenotype/disease.

• add.sibling(pheno) Adds a sibling to the family, with boolean parameter pheno indicating whether the sibling has the phenotype/disease.

• add.child(pheno) Adds a child to the family, with boolean parameter pheno indicating whether the child has the phenotype/disease.

• log.bayes.factor() Returns the overall log likelihood ratio (i.e. log Bayes-Factor) for this family.

Value

a new Family object

Examples

family <- new.family(
  maf=0.05,
  etiologic.fraction=0.8,
  penetrance=0.8,
  self="heterozygous",
  modus="dominant"
)
family$add.parent(pheno=TRUE)
family$add.parent(pheno=FALSE)
family$add.sibling(pheno=TRUE)
family$summary()

jweile/maveclin documentation built on May 4, 2019, 3:08 a.m.