mulParOpt {Mulcom} | R Documentation |
MulCom parameter optimization function to identify best combination of t and m providing maximum number of genes at a given FDR
mulParOpt(perm, M.Opt, ind, th, image = "T")
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 |
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.
Claudio Isella, claudio.isella@ircc.it
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)