Detection of global group effect

Description

Tests a global effect for a set of molecular features (e.g. genes, proteins,...) between the two groups of samples. Missing values are allowd in the expression data. Samples of the two groups are supposed to be unpaired.

Usage

  GlobTestMissing(X1, X2, nperm = 100)

Arguments

Value

The p-value of a permutation test.

Author(s)

Klaus Jung Klaus.Jung@ams.med.uni-goettingen.de

Examples

### Global comparison of a set of 100 proteins between two experimental groups,
### where (tau * 100) percent of expression levels are missing.
n1 = 10
n2 = 10
d = 100
tau = 0.1
X1 = t(matrix(rnorm(n1*d, 0, 1), n1, d))
X2 = t(matrix(rnorm(n2*d, 0.1, 1), n2, d))
X1[sample(1:(n1*d), tau * (n1*d))] = NA
X2[sample(1:(n2*d), tau * (n2*d))] = NA
GlobTestMissing(X1, X2, nperm=100)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(RepeatedHighDim)
Loading required package: MASS
Loading required package: nlme
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/RepeatedHighDim/GlobTestMissing.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GlobTestMissing
> ### Title: Detection of global group effect
> ### Aliases: GlobTestMissing
> 
> ### ** Examples
> 
> ### Global comparison of a set of 100 proteins between two experimental groups,
> ### where (tau * 100) percent of expression levels are missing.
> n1 = 10
> n2 = 10
> d = 100
> tau = 0.1
> X1 = t(matrix(rnorm(n1*d, 0, 1), n1, d))
> X2 = t(matrix(rnorm(n2*d, 0.1, 1), n2, d))
> X1[sample(1:(n1*d), tau * (n1*d))] = NA
> X2[sample(1:(n2*d), tau * (n2*d))] = NA
> GlobTestMissing(X1, X2, nperm=100)
$pval
[1] 0.27

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>