RHT (version 1.0)

RHT-package: Regularized Hotelling's T-square Test for Pathway (Gene Set) Analysis

Description

This package offers functions to perform regularized Hotelling's T-square test for pathway or gene set analysis. The package is tailored for but not limited to proteomics data, in which sample sizes are often small, and a large proportion of the data are missing and/or correlations may be present.

Details

Package:

RHT

Type:

Package

Version:

1.0

Date:

2011-11-14

License:

GPL

LazyLoad:

yes

References

Chen LS, Paul D, Prentice RL and Wang P. (2011) A regularized Hotelling's T-square test for pathway analysis in proteomics studies. Journal of the American Statistical Association, in press.

See Also

RHT.fun, RHT.2samp

Examples

 ## we simulate a data set with N=10 samples and p=50 proteins. 
  ## 20% of the data are missing.
  ## Among the 50 proteins, we randomly assign 2 pathways, with 5 and 12 proteins, respectively.
  
  set.seed(1)
  X <- matrix(rnorm(500),nrow=10)
  X[sample(1:500, 0.2*500)] <- NA
  path.idx <- list()
  path.idx[[1]] <- 1:5
  path.idx[[2]] <- 13:24
  names(path.idx) <- c("pathway A", "pathway B")
  
  ## The following function tests each pathway to see
  ## if any of the proteins in each pathway shows non-zero 
  ## abundance/expression
  
  pval <- RHT.fun(path.idx, dat=X)