simulation_Ic {BioTIP} | R Documentation

## calculating Ic scores based on simulated loci

### Description

simulate `x` loci `B` to calculate the Ic score, where x should be the same as the length of identified BioTiP and B is self-defined.

### Usage

    simulation_Ic(obs.x, sampleL, counts, B = 1000)

### Arguments

`obs.x` | A integer, length of identified BioTiP
`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'.
`counts` | A numeric matrix or dataframe in which columns are samples and rows are transcripts. Each row needs to have a unique row name (i.e. transcript ID)
`B` | A integer, setting the permutation with `B` runs. Default is 1000.

### Value

A matrix of `y` rows and `B` columns where `y` is the length of sampleL and `B` is self-defined. Each column is a set of Ic scores calculated for each state

### 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'])
    simulation_Ic(2,samplesL,counts,B =3)

[Package BioTIP version 1.0.0 Index]