PlotAllOneModel {WaveCGH}R Documentation

Plots all gain and loss regions in one one plot.

Description

This function finds break means for individual chromosome and then finds p-values by considering the residuals from all chromosomes as single series. Thereafter, it plots all the gain and loss regions in one plot.

Usage

PlotAllOneModel(x, Chromosome, ModelSelection = FALSE, nsim = 200, threshold = 0.05, qvalue = FALSE, ...)

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.
... Other arguments plot command.

Value

Plot of chromosome loss/gain regions.

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)
PlotAllOneModel(arrayCGH[(ch==1|ch==2),1], arrayCGH[(ch==1|ch==2),2])

[Package WaveCGH version 2.01 Index]