ExomeCopy-class: Class "ExomeCopy"

In exomeCopy: Copy number variant detection from exome sequencing read depth

Description

Object returned by exomeCopy

Objects from the Class

Objects can be created by calls of the form new("ExomeCopy").

Slots

sample.name:

Object of class "character": an identifier for the sample

type:

Object of class "character": the type of model used, either "exomeCopy" or "exomeCopyVar"

path:

Object of class "Rle": the index of the predicted state for each window

ranges:

Object of class "IRangesList": the corresponding ranges for the observed counts and covariates

O.norm:

Object of class "numeric": the input vector of counts divided by X * beta

log.odds:

Object of class "numeric": the log ratio of the emission probabilities along the predicted path over the emission probabilities of the normal state

fx.par:

Object of class "list": a list of the settings S, d, normal.state and fit.var

init.par:

Object of class "list": a list of the initial parameters goto.cnv, goto.normal, beta.hat and phi.hat

final.par:

Object of class "list": a list of the final parameters goto.cnv, goto.normal, beta (and gamma for exomeCopyVar)

counts:

Object of class "numeric": the number of evaluations of the log likelihood performed by optim

convergence:

Object of class "numeric": the integer for convergence of optim, 0 for convergence

nll:

Object of class "numeric": the final value of the negative log likelihood

Methods

plot

signature(x = "ExomeCopy", y = "missing"): ...

show

signature(object = "ExomeCopy"): ...

See Also

exomeCopy

Examples

showClass("ExomeCopy")

exomeCopy documentation built on Nov. 8, 2020, 7:45 p.m.