RJaCGH (version 1.2.5)

prob.seq: Joint posterior probabilities of alteration

Description

This function computes posterior joint probabilities of alteration for arbitrary (contiguous) sets of probes. They are computed counting the times the particular sequence of alterations have ocurred in the Viterbi paths of every MCMC sample.

Usage

prob.seq(obj, from, to, filename, alteration = "Gain")

Arguments

obj

An object of class 'RJaCGH', 'RJaCGH.genome' or 'RJaCGH.Chrom'

from

Index of the starting probe to compute joint probability.

to

Index of the ending probe to compute joint probaility.

filename

name of the file with the Viterbi paths (created with getSequence.

alteration

either 'Gain' or 'Loss'.

Value

• A joint probability of 'alteration' for the probes between 'from' and 'to'.

Details

Before using this function, a call to getSequence must be made in order to create the Viterbi paths. Note that the indexes for from and to are absolute, not relative to the chromosome.

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, pREC_A, link{}, pREC_S 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(0.5, 4), sigma.tau.sigma.2=rep(0.3, 4), sigma.tau.beta=rep(0.7, 4), tau.split.mu=0.5, tau.split.beta=0.5)

fit.genome <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="genome", burnin=10, TOT=1000, k.max = 4, jump.parameters=jp) getSequence(fit.genome, 'sequence', 'Gain') prob.seq(fit.genome, 1, 4, 'sequence', 'Gain')

models