transformDF: Transform Data Frame

In penetrance: Methods for Penetrance Estimation in Family-Based Studies

Transform Data Frame

Description

This function transforms a data frame from the standard format used in Fam3PRO into the required format which conforms to the requirements of penetrance (and clipp).

Usage

transformDF(df)

Arguments

df	The input data frame in the usual Fam3PRO format.

Details

This function implements a two-tier naming convention:

• User-facing input: uppercase 'Geno' (values 0 or 1)

• Internal processing: lowercase 'geno' (values "1/1" or "1/2")

The transformation converts 'Geno' = 1 (carrier) to 'geno' = "1/2", and 'Geno' = 0 (non-carrier) to 'geno' = "1/1". This separation provides clear distinction between user interface and internal implementation.

Value

A data frame in the format required for clipp with the following columns:

individual	ID of the individual
isProband	Indicator if the individual is a proband
family	Family ID
mother	Mother's ID
father	Father's ID
aff	Affection status
sex	Sex (2 for female, 1 for male)
age	Age at diagnosis or current age
geno	Genotype information (internal format)

Examples

# Create example data frame
df <- data.frame(
  ID = 1:2,
  PedigreeID = c(1,1),
  Sex = c(0,1),
  MotherID = c(NA,1),
  FatherID = c(NA,NA),
  isProband = c(1,0),
  CurAge = c(45,20),
  isAff = c(1,0),
  Age = c(40,NA),
  Geno = c(1,0)
)

# Transform the data frame
transformed_df <- transformDF(df)

penetrance documentation built on Sept. 9, 2026, 1:07 a.m.