visPed R package

An R package pedigree plotter based on the kinship2 and visNetwork R packages for families affected by multiple cancer syndromes. Designed to be compatible with the BayesMendel and associated packages.

Installation

Use the latest github version by running

devtools::install_github("bayesmendel/visPed")
library(visPed)

Usage

Pass a compatible pedigree (data frame) into the function.

visPed(pedigree)

To view the pedigree as a hierarchical network, which relies on the visNetwork package, run

toVisNetwork(pedigree)

Pedigree specifications

The user must specify the pedigree argument as a data frame with the following columns:

• ID: A numeric value; ID for each individual. There should not be any duplicated entries.
• Sex: A numeric value; 0 for female and 1 for male. Missing entries are not currently supported.
• MotherID: A numeric value; unique ID for someone’s mother.
• FatherID: A numeric value; unique ID for someone’s father.
• isProband: A numeric value; 1 if someone is a proband, 0 otherwise. This will be overridden by the proband argument in PanelPRO, if it is specified. At least one proband should be specified by either the isProband column or proband. Multiple probands are supported.
• CurAge: A numeric value; the age of censoring (current age if the person is alive or age of death if the person is dead). Ages ranging from 1 to 94 are allowed.
• isAffX: A numeric value; the affection status of cancer X, where X is a short cancer code (see below). Affectation status should be encoded as 1 if the individual was diagnosed, 0otherwise. Missing entries are not currently supported.
• AgeX: A numeric value; the age of diagnosis for cancer X, where X is a short cancer code (see below). Ages ranging from 1 to 94 are allowed. If the individual was not diagnosed for a given cancer, their affectation age should be encoded as NA and will be ignored otherwise.
• isDead: A numeric value; 1 if someone is dead, 0 otherwise. Missing entries are assumed to be 0.