diseaseModel: Disease models for linkage analysis

Description Usage Arguments Value See Also Examples

View source: R/diseaseModel.R

Description

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

Usage

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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

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# 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 May 5, 2021, 1:08 a.m.