mulParOpt {Mulcom} | R Documentation

## MulCom Parameters Optimization

### Description

MulCom parameter optimization function to identify best combination of t and m providing maximum number of genes at a given FDR

### Usage

       mulParOpt(perm, M.Opt, ind, th, image = "T")

### Arguments

`perm` | a object with permutated MulCom Scores
`M.Opt` | an MulCom optimization object
`ind` | index corresponding to the comparison to plot
`th` | a threshold for the FDR plot
`image` | default = "T", indicates is print the MulCom optimization plot

### Details

`mulParOpt` The function mulParOpt is designed to identify the optimal m and t values combination leading to the maximum number of differentially regulated genes satisfying an user define FDR threshold. In case of equal number of genes, the combination of m and t with the lower FDR will be prioritized. In case of both identical number of genes and FDR, the function will chose the highest t. The function optionally will define a graphical output to visually inspect the performance of the test at given m and t parameters for a certain comparison.

### Author(s)

Claudio Isella, claudio.isella@ircc.it

### Examples

       data(benchVign)
       mulcom_perm <- mulPerm(Affy, Affy$Groups, 10,2)
       mulcom_opt <- mulOpt(mulcom_perm, vm=seq(0.1, 0.5, 0.1), vt=seq(1, 3,1))
       mulParOpt(mulcom_perm, mulcom_opt, 1, 0.05)

[Package Mulcom version 1.30.0 Index]