PvalBootMeanChr {WaveCGH}R Documentation

Finds p-values for testing means in individual chromosomes.

Description

This function applies maximum overlap discrete wavelet transform (MODWT) to find break means inside each of the chromosomes. Then applies bootstrap method to find p-values for testing the means.

Usage

PvalBootMeanChr(x, Chromosome, ModelSelection = FALSE, nsim = 200)

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.

Value

Vector of p-values of length equal to that of original series.

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

[Package WaveCGH version 2.01 Index]