print.pMCR.RJaCGH {RJaCGH} | R Documentation |
A print method for pMCR
objects
## S3 method for class 'pMCR.RJaCGH': print(x,...) ## S3 method for class 'pMCR.RJaCGH.Chrom': print(x,...) ## S3 method for class 'pMCR.RJaCGH.genome': print(x,...) ## S3 method for class 'pMCR.RJaCGH.array': print(x,...) ## S3 method for class 'pMCR.RJaCGH.array.Chrom': print(x,...) ## S3 method for class 'pMCR.RJaCGH.array.genome': print(x,...)
x |
An object of class pMCR.RJaCGH ,
pMCR.RJaCGH.Chrom , pMCR.RJaCGH.genome ,
pMCR.RJaCGH.array , pMCR.RJaCGH.array.Chrom or
pMCR.RJaCGH.array.genome .
|
... |
Additional arguments passed to 'print'. Currently ignored. |
A matrix 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, number of genes in it and joint probability.
Oscar M. Rueda and Ramon Diaz Uriarte
Oscar M. Rueda and Ramon Diaz Uriarte. A flexible, accurate and extensible statistical method for detecting genomic copy-number changes. http://biostats.bepress.com/cobra/ps/art9/ {http://biostats.bepress.com/cobra/ps/art9/}.
RJaCGH
,
states
, model.averaging
,
pMCR
## MCR for a single array: 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.genome <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="genome", burnin=100, TOT=1000, jump.parameters=jp, k.max = 4) pMCR(fit.genome, p=0.8, alteration="Gain") pMCR(fit.genome, p=0.8, alteration="Loss") ##MCR for two arrays: z <- c(rnorm(110, 0, 1), rnorm(20, 3, 1), rnorm(100,0, 1)) fit.array.genome <- RJaCGH(y=cbind(y,z), Pos=Pos, Chrom=Chrom, model="genome", burnin=100, TOT=1000, jump.parameters=jp, k.max = 4) pMCR(fit.array.genome, p=0.4, alteration="Gain") pMCR(fit.array.genome, p=0.4, alteration="Loss")