example.geno: Example datasets for pedgene

In pedgene: Gene-Level Variant Association Tests for Pedigree Data

Example datasets for pedgene

Description

example.geno: a data frame with minor allele count for subjects (rows) at variant positions (columns); example.ped: pedigree and trait data for subjects in example.geno; example.map: gene and chromosome for variant positions in example.geno; example.relation: special (twin) relationships for individuals in example.ped

Usage

data(example.geno)
data(example.ped)
data(example.map)
data(example.relation)

Format

example.geno -data frame with minor allele count for 20 variant positions:

ped

pedigree ID, character or numeric

person

person ID, used with ped to match subjects to their row in example.ped

AA.1-AA.10,AX.1-AX.10

genotype columns at 10 positions for each of 2 simulated genes

example.ped -data frame with pedigree structure and trait values in the following columns:

ped

pedigree ID, character or numeric

person

person ID, a unique ID within each pedigree

father

father ID, 0 if no father

mother

mother ID, 0 if no mother

sex

coded as 1 for male, 2 for female

trait

phenotype, either case-control status coded as 1 for affected and 0 for unaffected, or a continuous value. Subjects with missing (NA) will be removed from the analysis

trait.adjusted

an optional variable for covariate-adjusted trait. If trait.adjusted is present in the data.frame, then gene-level tests are adjusted for covariates using residuals = (trait - trait.adjusted). Otherwise, gene-level tests are not adjusted for covariates, in which case residuals = trait - mean(trait)

example.map - data frame with columns for gene name and chromosome:

chrom

chromosome code (1-23,X allowed) where the gene is located

gene

gene identifier

example.relation - matrix specifying special relationships between pairs of individuals in the following columns:

ped

pedigree ID, character or numeric

id1

person1 ID, used with ped to match subjects to their row in example.ped

id2

person2 ID, used with ped to match subjects to their row in example.ped

code

any of the following: 1=Monozygotic twin, 2=Dizygotic twin, 3=Twin of unknown zygosity, and 4=Spouse

Source

Simulated data for testing purposes

Examples

data(example.geno)
data(example.ped)
data(example.map)
data(example.relation)

pedgene documentation built on Sept. 9, 2025, 5:52 p.m.