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]