paramlink (version 0.7-0)

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

Description

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

Usage

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

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

Arguments

x

in setModel: a linkdat object. In print.linkdat.model: a linkdat.model object, as described below.

model

NULL, or an object of class linkdat.model, namely a list with elements chrom, penetrances, dfreq, nallel, afreq. In the setModel function, the model

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 - (f_0, f_1, f_2) - where f_i is the probability of being affected given i disease alleles. If chrom=='X': a list of length two containing the

dfreq

the population frequency of the disease allele.

nallel

the number of alleles at the marker loci. At the moment only diallelic SNPs are allowed in likelihood calculations.

afreq

a numeric of length nallel - the population allele frequencies at the marker loci.

...

further parameters

Value

• a linkdat object equal to x, except that its model entry is set according to the given parameters.

See Also

linkdat

Examples

data(toyped)
x = linkdat(toyped)
x = setModel(x, model=1)
summary(x)
y = setModel(x, model=4, dfreq=0.1)
summary(y)