mutInfTest: Test for mutual information

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

View source: R/entropyFunctions.r

Description

A test evaluates the significance of the mutual information between two (high-dimensional) multivariate random variables. The null distribution is obtained via an efficient permutation resampling algorithm.

Usage

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mutInfTest(Y, X, nPerm = 1000, method = "normal", k = 1, center = TRUE, 
rescale = TRUE, lowCiThres=0.10, ncpus=1, verbose=FALSE)

Arguments

Y

(High-dimensional) matrix. Columns are assumed to represent the samples, and rows represent the samples' genes or traits.

X

(High-dimensional) matrix. Columns are assumed to represent the samples, and rows represent the samples' genes or traits. The number of columns of X must be identical to that of Y.

nPerm

Number of permutations.

method

Distributional assumption under which mutual information is to be estimated.

k

k-nearest neighbor parameter.

center

Logical indicator: should the rows of Y and X be centered at zero? Applied only under the normality assumption.

rescale

Logical indicator: should Y and X be rescaled to have the same scale? Applied only under the k-NN assumption.

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 miTest-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.

See Also

hdMI

Examples

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# load data
data(pollackCN16) 
data(pollackGE16) 
Y <- t(exprs(pollackGE16)) 
X <- t(copynumber(pollackCN16)) 

# perform testing and print test results
testRes <- mutInfTest(Y, X, nPerm = 1000) 
summary(testRes) 

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