PlotLatticeOneModel {WaveCGH} | R Documentation |
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.
PlotLatticeOneModel(x, Chromosome, PlotChrom = Unique(Chromosome), ModelSelection = FALSE, nsim = 200, threshold = 0.05, qvalue = FALSE, Panel = c(1, 1), ...)
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. |
Plot of gain/loss regions for each chromosome.
A. I. McLeod and M. S. Islam
Islam, M. S. (2008). Periodicity, Change Detection and Prediction in Microarrays. Ph.D. Thesis, The University of Western Ontario.
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))