simulationMCI {BioTIP} | R Documentation

## Get MCI Scores for Feature Permutation

### Description

This function gets the MCI scores for randomly selected features (e.g. transcript ids)

### Usage

    simulationMCI(len, samplesL, df, adjust.size = FALSE, B = 1000)

### Arguments

`len` | A integer that is the length of BioTiP.
`samplesL` | A list of vectors, whose length is the number of states. Each vector gives the sample names in a state. Note that the vector s (sample names) has to be among the column names of the R object 'df'.
`df` | A numeric matrix or dataframe of numerics, factor or character. The rows and columns represent unique transcript IDs (geneID) and sample names, respectively
`adjust.size` | A boolean value indicating if MCI score should be adjust by module size (the number of transcripts in the module) or not. Default FALSE.
`B` | A integer, setting the permutation with `B` runs. Default is 1000.

### Value

A numeric matrix indicating the MCI scores of permutation. The dimemsion (row * column) of this matrix is the length of `samplesL` * `B`.

### Author(s)

Zhezhen Wang zhezhen@uchicago.edu

### Examples

    counts = matrix(sample(1:100,18),3,9)
    colnames(counts) = 1:9
    row.names(counts) = c('loci1','loci2','loci3')
    cli = cbind(1:9,rep(c('state1','state2','state3'),each = 3))
    colnames(cli) = c('samples','group')
    samplesL <- split(cli[,1],f = cli[,'group'])
    simMCI = simulationMCI(2,samplesL,counts,B=2)

[Package BioTIP version 1.0.0 Index]