score.fam: Given a relationship matrix and status dataframe, score a...

In KinformR: Relationship-Informed Pedigree and Variant Scoring

Given a relationship matrix and status dataframe, score a family by applying the calc.rv.score scoring system to every pairwise combination of individuals.

Description

By default all individuals are treated as the reference 'proband' and the given variant's score is calculated based on relationships to all other individuals. e.g. for each row in the relationship matrix. calc.rv.score is run, with the row name indicating the reference individual that the calculation is relative to. Note that the relation.mat can include more individuals than are present within the status.df, but the matrix will be subset to include only those individuals that have status information provided.

Usage

score.fam(
  relation.mat,
  status.df,
  affected.weight = 1,
  unaffected.weight = 0.5,
  return.sums = FALSE,
  return.means = TRUE,
  affected.only = TRUE,
  max.err = 4
)

Arguments

relation.mat	A relationship matrix for the family.
status.df	A dataframe with the encoded variant/disease status of each individual
affected.weight	A coefficient to multiply the calculated A.c and A.i relatedness values by.
unaffected.weight	A coefficient to multiply the U.c and U.i relatedness values by.
return.sums	Boolean indicating if sum of family variant scores should be returned (default = FALSE).
return.means	Boolean indicating if mean of all family variant scores should be returned (default = TRUE).
affected.only	Boolean indicating if family score should be calculated using only affected individuals (default = TRUE).
max.err	A heuristic cap of the number of incorrect assignments allowed when scoring. When the total number of incorrect (sum of affected and unaffected) is exceeded, the variant's score is set to 0, regardless of the number of points for or against. This simplifies scoring and allows for fast filtering of poor quality variants. Default is 4.

Details

There are several return options possible.

• If affected.only is TRUE, the final scores will be reported for only rows where the reference individual is affected (default = True).

• If return.means is TRUE, the average scores for the rows will be reported. (default = TRUE)

• If return.sums is True, the sum of the scores for all the rows will be reported. (default = False) NOTE: if affected.only = True, the averages and sums are calculated using only the affected reference individuals.

Value

A labelled vector with names: score, score.for, score.against

Examples

mat.name1 <- system.file("extdata/1234_ex2.mat", package = "KinformR")
tsv.name1 <- system.file("extdata/1234_ex2.tsv", package = "KinformR")
mat.df <- read.relation.mat(mat.name1)
ind.df <- read.indiv(tsv.name1)
ind.df.status <- score.variant.status(ind.df)
score.default <- score.fam(mat.df, ind.df.status)

KinformR documentation built on Feb. 17, 2026, 5:07 p.m.