PlotLatticeOneModel {WaveCGH}R Documentation

Plots all gain and loss regions in separate plots for each chromosome.

Description

This function finds break means for individual chromosome and then finds p-values for testing means by considering the residuals from all chromosomes to be a single series. Thereafter, it plots all the gain and loss regions in separate plots.

Usage

PlotLatticeOneModel(x, Chromosome, PlotChrom = Unique(Chromosome), ModelSelection = FALSE, nsim = 200, threshold = 0.05, qvalue = FALSE, Panel = c(1, 1), ...)

Arguments

x Array-CGH data.
Chromosome Sequence of chromosomes, eg. 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3 and so on.
PlotChrom which chromosomes to plot.
ModelSelection Whether to estimate order (p) of an AR(p) process.
nsim Number of bootstrap simulations.
threshold FDR threshold for multiple comparison.
qvalue Whether to use Storey's q-value approach or not.
Panel The format of plotting the chromosomes.
... Other arguments plot command.

Value

Plot of gain/loss regions for each chromosome.

Author(s)

A. I. McLeod and M. S. Islam

References

Islam, M. S. (2008). Periodicity, Change Detection and Prediction in Microarrays. Ph.D. Thesis, The University of Western Ontario.

Examples

data(arrayCGH)
ch<- arrayCGH[,2]
# We use first and second chromosomes
set.seed(123)
PlotLatticeOneModel(arrayCGH[(ch==1|ch==2),1], arrayCGH[(ch==1|ch==2),2], Panel=c(1,2))

[Package WaveCGH version 2.01 Index]