PlotAllOneModel {WaveCGH} | R Documentation |
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.
PlotAllOneModel(x, Chromosome, ModelSelection = FALSE, nsim = 200, threshold = 0.05, qvalue = FALSE, ...)
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. |
Plot of chromosome loss/gain regions.
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) PlotAllOneModel(arrayCGH[(ch==1|ch==2),1], arrayCGH[(ch==1|ch==2),2])