pedgene (version 2.9)

example.geno: 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

Usage

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

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

Examples

# NOT RUN {
data(example.geno)
data(example.ped)
data(example.map)
# }