diseaseModel: Disease models for linkage analysis

In paramlink2: Parametric Linkage Analysis

Disease models for linkage analysis

Description

Create a disease model in form of a disModel object, for use in e.g. lod().

Usage

diseaseModel(model = NULL, chrom = NULL, penetrances = NULL, dfreq = NULL)

Arguments

model	An existing disModel object (to be modified by other arguments), or one of the following two-letter keywords: AD = autosomal dominant AR = autosomal recessive XD = X-linked dominant XR = X-linked recessive In all of the above, the disease is assumed to be fully penetrant, and with a disease allele frequency of 1e-5.
chrom	Either "AUTOSOMAL" or "X". Lower case versions are allowed and will be converted automatically.
penetrances	For autosomal models, a numeric of length 3 corresponding to (f0, f1, f2), where fi is the probability of being affected given i disease alleles. It can also be a matrix with 3 columns, in which case each row represents a liability class. For X-linked models, a list of two vectors named male and female, of lengths 2 and 3 respectively: (f0, f1) for males and (f0, f1, f2) for females. Alternatively, each list entry may be a matrix or data frame (with the same number of columns) where each row represents a liability class.
dfreq	A number in [0,1]: The population frequency of the disease allele.

Value

An object of class disModel, which is a list with entries chrom, penetrances and dfreq.

See Also

lod()

Examples

# Fully penetrant AD model:
m1 = diseaseModel(model = "AD")

# The above is equivalent to
m2 = diseaseModel(chrom = "Aut", penetrances = c(0,1,1), dfreq = 1e-5)
stopifnot(identical(m1, m2))

# X-linked recessive model:
m3 = diseaseModel(model = "XR", dfreq = 0.01)

# Long version of the above:
m4 = diseaseModel(chrom = "X", penetrances = list(male = c(0,1), female = c(0,0,1)),
              dfreq = 0.01)
stopifnot(identical(m3, m4))

paramlink2 documentation built on Feb. 16, 2023, 6:05 p.m.