setModel: Set, change or display the model parameters for 'linkdat'...

In paramlink: Parametric Linkage and Other Pedigree Analysis in R

Set, change or display the model parameters for 'linkdat' objects

Description

Functions to set, change and display model parameters involved in parametric linkage analysis.

Usage

setModel(x, model = NULL, chrom = NULL, penetrances = NULL, dfreq = NULL)

## S3 method for class 'linkdat.model'
print(x, ...)

Arguments

x	in setModel: a linkdat object. In print.linkdat.model: a linkdat.model object.
model	NULL, or an object of class linkdat.model, namely a list with elements chrom, penetrances and dfreq. In the setModel function, the model argument can be one of the integers 1-4, with the following meanings: 1 = autosomal dominant; fully penetrant, dfreq=1e-5 2 = autosomal recessive; fully penetrant, dfreq=1e-5 3 = X-linked dominant; fully penetrant, dfreq=1e-5 4 = X-linked recessive; fully penetrant, dfreq=1e-5
chrom	a character, either 'AUTOSOMAL' or 'X'. Lower case versions are allowed and will be converted automatically.
penetrances	if chrom=='AUTOSOMAL': a numeric of length 3 - (f0, f1, f2) - where fi is the probability of being affected given i disease alleles. If chrom=='X': a list of two vectors, containing the penetrances for each sex: penetrances = list(male=c(f0, f1), female=c(f0, f1, f2)).
dfreq	the population frequency of the disease allele.
...	further parameters

Value

setModel returns a new linkdat object, whose model entry is a linkdat.model object: A list containing the given chrom, penetrances and dfreq.

See Also

linkdat

Examples

data(toyped)
x = linkdat(toyped)
x1 = setModel(x, model=1)
summary(x1)

# The shortcut 'model=1' above is equivalent to
x2 = setModel(x, chrom='AUTOSOMAL', penetrances=c(0,1,1), dfreq=1e-5)
stopifnot(all.equal(x1, x2))

# X-linked recessive model:
y1 = setModel(x, model=4, dfreq=0.01)
summary(y1)

# Long version of the above:
y2 = setModel(x, chrom='X', penetrances=list(male=c(0,1), female=c(0,0,1)),
              dfreq=0.01)
stopifnot(all.equal(y1, y2))

stopifnot(all.equal(y1, setModel(x, y1$model)))

paramlink documentation built on April 15, 2022, 9:06 a.m.