origin: Parent of origin testing

In chr1swallace/origin: Parent of origin testing

Description

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

Usage

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

##---- 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.