HmmOptions-class {VanillaICE} | R Documentation |
Options for fitting the hidden Markov model.
Objects can be created by calls of the form new("HmmOptions", snpset, states, copyNumber.location, copyNumber.scale, copyNumber.ICE, calls.ICE, probHomCall, term5)
.
states
:"character"
. Hidden
states of the HMM.snpset
:"SnpLevelSet"
instance. copyNumber.location
:"numeric"
. Ignored when snpset is an instance of
SnpCallSet
. See copyNumber.location
copyNumber.scale
:"NULLOrNumeric"
. This slot is not currently used. If one
has standard errors for the copy number estimates, the inverse of
the standard errors should be stored in the cnConfidence
assayData
element of the snpset object.copyNumber.ICE
:"logical"
. See copyNumber.ICE
. calls.ICE
:"logical"
. See calls.ICE
probHomCall
:"numeric"
. The
probability of a homozygous genotype call corresponding to each of
the states. When calls.ICE
is TRUE, only the first two
elements will be used.term5
:"NULLOrNumeric"
. User-specified probabilities of f(HOM |
genotype call, state). Ignored when
calls.ICE
is FALSE
. For more details, see Equation
2.7 in the manuscript that this package references.signature(x = "HmmOptions")
: signature(object = "HmmOptions")
: signature(object = "HmmOptions", value = "ANY")
: signature(object = "HmmOptions")
: signature(object = "HmmOptions")
: signature(object = "HmmOptions", value="logical")
: signature(object = "HmmOptions")
: signature(object = "HmmOptions", value="logical")
: signature(object = "HmmOptions")
: signature(object = "HmmOptions", params = "HmmParameter")
:signature(.Object = "HmmOptions")
: signature(object = "HmmOptions")
: signature(object = "HmmOptions")
: signature(object = "HmmOptions")
: signature(object = "HmmOptions", value = "character")
: R. Scharpf
showClass("HmmOptions")