getIc {BioTIP} | R Documentation

## get Ic score

### Description

retreive Ic scores (Pearson correlation of genes / Pearson correlation of samples) for the identified BioTiP

### Usage

    getIc(counts, sampleL, genes, output = c("Ic", "PCCg", "PCCs"))

### Arguments

`counts` | A numeric matrix or data frame. The rows and columns represent unique transcript IDs (geneID) and sample names, respectively.
`sampleL` | 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'.
`genes` | A character vector consisting of unique BioTiP ids. This can be obtained from `getMaxMCImember`
`output` | A string. Please select from 'Ic', 'PCCg', or 'PCCs'. Uses 'Ic' by default. 'PCCg' is the PCC between genes (numerator) and 'PCCs' is PCC between samples (denominator)

### Value

A list of numeric values, whose length and names are inherited from `sampleL`

### Author(s)

Zhezhen Wang zhezhen@uchicago.edu

### Examples

    counts = matrix(sample(1:100,27),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'])
    BioTiP = c('loci1','loci2')
    Ic = getIc(counts,samplesL,BioTiP)

[Package BioTIP version 1.0.0 Index]