fitNaiveGenotypes {aroma.light} | R Documentation |
Fit naive genotype model from a normal sample
Description
Fit naive genotype model from a normal sample.
Usage
## S3 method for class 'numeric'
fitNaiveGenotypes(y, cn=rep(2L, times = length(y)), subsetToFit=NULL,
flavor=c("density", "fixed"), adjust=1.5, ..., censorAt=c(-0.1, 1.1), verbose=FALSE)
Arguments
y |
A numeric vector of length J containing allele B fractions
for a normal sample.
|
cn |
An optional numeric vector of length J specifying the true
total copy number in \{0,1,2,NA\} at each locus. This can be
used to specify which loci are diploid and which are not, e.g.
autosomal and sex chromosome copy numbers.
|
subsetToFit |
An optional integer or logical vector specifying
which loci should be used for estimating the model.
If NULL , all loci are used.
|
flavor |
A character string specifying the type of algorithm used.
|
adjust |
A positive double specifying the amount smoothing for
the empirical density estimator.
|
... |
Additional arguments passed to findPeaksAndValleys ().
|
censorAt |
A double vector of length two specifying the range
for which values are considered finite. Values below (above) this
range are treated as -Inf (+Inf ).
|
verbose |
A logical or a Verbose object.
|
Value
Returns a list
of list
s.
Author(s)
Henrik Bengtsson
See Also
To call genotypes see callNaiveGenotypes
().
Internally findPeaksAndValleys
() is used to identify the thresholds.
[Package
aroma.light version 3.24.0
Index]