Mulcom (version 1.22.0)

mulParOpt: 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.

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)