Description Details Author(s) References See Also Examples
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.
Package: | RHT |
Type: | Package |
Version: | 1.0 |
Date: | 2011-11-14 |
License: | GPL |
LazyLoad: | yes |
Lin S. Chen and Pei Wang
Maintainer: Lin S. Chen <lchen11@uchicago.edu>
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## 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)
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