origin: Parent of origin testing

Description Usage Arguments Value Author(s) References Examples

Description

Parent of origin testing using the method proposed by Weinberg, with extension to accomodate more than one affeected offspring in a family.

Usage

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origin(genotype, data = sys.frame(sys.parent()), pedigree, id,
              id.father, id.mother, affected, codes = 2, first = FALSE,
              verbose = TRUE)

Arguments

genotype

factor with 3 levels or another object which can be coerced to a factor with 3 levels describing genotype. NB if coerced to a factor, it is assumed the levels are ordered so that the heterozygote appears in the middle

data

data.frame containing genotype (and other variables) if not in current environment.

pedigree

name of the variable grouping individuals from the same nuclear family

id

name of the variable identifying subjects within pedigrees

id.father

id of subject's father (0 indicates this subject has no father in the pedigree)

id.mother

id of subject's mother (0 indicates this subject has no mother in the pedigree)

affected

whether an individual is affected. See codes.

codes

value(s) of affected variable which indicates subject is affected. All other values (apart from NA) will be assumed unaffected.

first

if TRUE only the first affected subject with genotype data will be used in each pedigree.

verbose

if TRUE print out (hopefully) useful information as data is reformatted for the parent of origin test.

Value

The return value is a list, with class c("list", "origin"). Its entries are:

M3

Model with imprinting + maternal genotype effects

M2

Model with maternal genotype effects

M1

Model with imprinting effect

M0

Model with no effect (for completeness)

A print method is defined, which prints a summary of the models and their deviance. To access the individual models, do: models<-origin(snp,data=mydata) print(models) ## print comparison models$M3 ## print full model summary(models$M1) ## print imprinting model with some detail

Author(s)

Chris Wallace

References

Weinberg et al. Methods for detection of parent-of-origin effects in genetic studies of case-parents triads. Am J Hum Genet 65:229-235. 1999.

Wallace et al. The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes. Nat Genet. http://dx.doi.org/doi:10.1038/ng.493

Examples

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##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

chr1swallace/origin documentation built on May 13, 2019, 6:19 p.m.