Description Usage Arguments Value Author(s) References See Also Examples

View source: R/entropyFunctions.r

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.

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

`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 |

`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 |

`k1` |
k-nearest neighbor parameter for group comprising of samples indicated by a one in the indicator variable |

`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 |

`ncpus` |
Number of cpus used for the permutations. |

`verbose` |
Logical indicator: should intermediate output be printed on the screen? |

Object of `entTest`

-class.

Wessel N. van Wieringen: [email protected]

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.

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)
``` |

```
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: CGHbase
Loading required package: marray
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: mvtnorm
Two-sample entropy test:
Test statistic: -6.686, p-value: 1
Remarks: resampling terminated prematurely: unlikely significance
```

sigaR documentation built on May 6, 2019, 3:40 a.m.

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