PlotLattice {WaveCGH}R Documentation

Plots all gain and loss regions in separate plots for chromosomes.

Description

This function finds break means for individual chromosome and then finds p-values for testing means. Thereafter, it plots all the gain and loss regions in separate plots.

Usage

PlotLattice(x, 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.
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)
PlotLattice(arrayCGH[(ch==1|ch==2),1], arrayCGH[(ch==1|ch==2),2], Panel=c(1,2))

[Package WaveCGH version 2.01 Index]