# entropyTest: One-sided two-sample test for entropy comparison In sigaR: Statistics for Integrative Genomics Analyses in R

## Description

A one-sided two-sample test compares the entropy of a (high-dimensional) multivariate random variable between two groups. The test is one-sided: one group is a priori suspected to have a larger entropy. The null distribution is obtained via an efficient permutation resampling algorithm.

## Usage

 ```1 2``` ```entropyTest(Y, id, nPerm = 1000, method = "normal", k0 = 1, k1 = 1, center = TRUE, lowCiThres=0.10, ncpus=1, verbose=FALSE) ```

## Arguments

 `Y` (High-dimensional) matrix. Rows are assumed to represent the samples, and columns represent the samples' genes or traits. `id` An indicator variable for the two groups to be compared. The groups should be coded as `0` and `1`. There is an asymmetric interest in the groups: the group indicated by `1` is believed to exhibit a larger entropy. `nPerm` Number of permutations. `method` Distributional assumption under which entropy is to be estimated. `k0` k-nearest neighbor parameter for group comprising of samples indicated by a zero in the indicator variable `id`. `k1` k-nearest neighbor parameter for group comprising of samples indicated by a one in the indicator variable `id`. `center` Logical indicator: should the columns of Y be centered around zero? `lowCiThres` A value between 0 and 1. Determines speed of efficient p-value calculation. If the probability of a p-value being below `lowCiThres` is smaller than 0.001 (read: the test is unlikely to become significant), the permutation analysis is terminated and a p-value of 1.00 is reported. `ncpus` Number of cpus used for the permutations. `verbose` Logical indicator: should intermediate output be printed on the screen?

## Value

Object of `entTest`-class.

## Author(s)

Wessel N. van Wieringen: [email protected]

## References

Van Wieringen, W.N., Van der Vaart, A.W. (2011), "Statistical analysis of the cancer cell's molecular entropy using high-throughput data", Bioinformatics, 27(4), 556-563.

Van Wieringen, W.N., Van de Wiel, M.A., Van der Vaart, A.W. (2008), "A test for partial differential expression", Journal of the American Statistical Association, 103(483), 1039-1049.

`hdEntropy`

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10``` ```# load data data(pollackGE16) Y <- exprs(pollackGE16) # assign samples to groups id <- sample(c(0,1), 41, replace=TRUE) # perform testing and print test results testRes <- entropyTest(t(Y), id, nPerm = 5, method="knn") summary(testRes) ```

### Example output

```Loading required package: Biobase

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pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
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which.max, which.min

Welcome to Bioconductor

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