relabelStates {RJaCGH} | R Documentation

## Relabelling of hidden states to biological states of alteration.

### Description

For every model, each hidden state is assigned to a state of copy number alteration ('normal', 'loss1', 'loss2', 'gain1', 'gain2'...)

### Usage

    relabelStates(obj, normal.reference = 0,
                  window = NULL, singleState = FALSE,
    array=NULL, Chrom=NULL)
    ## S3 method for class 'RJaCGH'
    relabelStates(obj, normal.reference = 0,
                                   window = NULL, singleState = FALSE,
    array=NULL, Chrom=NULL)

### Arguments

`obj` | An object returned from RJaCGH() of class 'RJaCGH', 'RJaCGH.Chrom', 'RJaCGH.Genome'.
`normal.reference` | The value considered as the mean of the normal state. See details. By default is `0`.
`window` | Multiplier of the standard deviation of the data to dtermine the width of the normal state. See details. Default (window = NULL) is 1.
`singleState` | If TRUE, each state is assigned a probability of 1 of being Gained or Lost or Normal, and 0 of being anyting else. This mimics the behavior of previous versions of RJaCGH. See details.
`array` | Vector of arrays to be relabeled. If NULL, all of them.
`Chrom` | Vector of chromosome to be relabeled (only if a different model has been fitted to each of them). If NULL, all of them are labeled.

### Details

A relabelling of hidden states is performed to match biological states. We first define an upper and lower limit as: normal.reference +/- window. Next, we compute as the probability that a given state is gained the area beyond the upper limit, and the area up to the lower limit as the probability that a given state is lost. The areas are obtained from a Normal with posterior estimates of mean and standard deviation for each hidden state. The probability of being in a normal state is defined as 1 - prob.gained - prob.loss.

Labels are assigned based on the state with highest probability. If we set singleState = TRUE, all the probability is assigned to a single condition, the one with largest probability.

### Value

An object of the same class as `obj` with hidden states relabelled.

### Author(s)

Oscar M. Rueda and Ramon Diaz Uriarte

### References

Rueda OM, Diaz-Uriarte R. Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH. PLoS Comput Biol. 2007;3(6):e122

### See Also

`RJaCGH`

### Examples

    y <- c(rnorm(100, 0, 1), rnorm(10, -3, 1), rnorm(20, 3, 1),
           rnorm(100,0, 1))
    Pos <- sample(x=1:500, size=230, replace=TRUE)
    Pos <- cumsum(Pos)
    Chrom <- rep(1:23, rep(10, 23))

    jp <- list(sigma.tau.mu=rep(0.05, 4), sigma.tau.sigma.2=rep(0.03, 4),
               sigma.tau.beta=rep(0.07, 4), tau.split.mu=0.1, tau.split.beta=0.1)

    fit.chrom <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="Chrom",
                        burnin=10, TOT=1000, k.max = 4,
                        jump.parameters=jp)
    plot(fit.chrom)
    fit.chrom.2 <- relabelStates(fit.chrom, normal.reference=3)
    plot(fit.chrom.2)

[Package RJaCGH version 2.0.4 Index]