print.pREC_S: Method for printing probabilistic common regions

In RJaCGH: Reversible Jump MCMC for the Analysis of CGH Arrays

Description

A print method for pREC_S objects.

Usage

## S3 method for class 'pREC_S'
print(x,...)
## S3 method for class 'pREC_S.Chromosomes'
print(x,...)
## S3 method for class 'pREC_S.none'
print(x,...)

Arguments

x	An object of class pREC_S, pREC_S.Chromosomes or pREC_S.none.
...	Additional arguments passed to print. Currently ignored.

Value

A data.frame is printed with as many rows as regions found and with columns containing chromosome where the region is, position of start and end of the region and the arrays that belong to the region.

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

pREC_S

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)

z <- c(rnorm(110, 0, 1), rnorm(20, 3, 1),
       rnorm(100,0, 1)) 
zz <- c(rnorm(90, 0, 1), rnorm(40, 3, 1),
       rnorm(100,0, 1)) 

fit.array.genome <- RJaCGH(y=cbind(y,z,zz),
Pos=Pos, Chrom=Chrom, model="genome",
burnin=1000, TOT=1000, jump.parameters=jp, k.max = 4)
pREC_S(fit.array.genome, p=0.4, freq.array=2,
alteration="Gain")
pREC_S(fit.array.genome, p=0.4, freq.array=2, alteration="Loss")

RJaCGH documentation built on May 2, 2019, 3:34 p.m.