Description Usage Arguments Value Author(s) References See Also Examples
This function tests if a pathway (or gene set) consists of any protein (or gene) that shows non-zero abundance (or expression).
1 | RHT.fun(path.idx, dat, nsim = 1000, seed = 123)
|
path.idx |
This is a LIST. Each element in the list contains the indice of proteins (or genes) for a pathway in the data set. |
dat |
An N by p matrix of protein abundance (or gene expression). Each row represents one sample and each column represents a protein (or a gene). |
nsim |
Number of resamples needed to calculate the p-value. By default, nsim=1000. |
seed |
A single integer that controls the random number generator in the resampling. |
The function returns the p-values for each pathway in the list path.idx
.
Lin S Chen and Pei Wang
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.2samp
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## 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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