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