setModel | R Documentation |
Functions to set, change and display model parameters involved in parametric linkage analysis.
setModel(x, model = NULL, chrom = NULL, penetrances = NULL, dfreq = NULL) ## S3 method for class 'linkdat.model' print(x, ...)
x |
in |
model |
NULL, or an object of class 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 If |
dfreq |
the population frequency of the disease allele. |
... |
further parameters |
setModel
returns a new linkdat
object, whose
model
entry is a linkdat.model
object: A list containing the
given chrom
, penetrances
and dfreq
.
linkdat
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)))
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