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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(Mulcom)
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following objects are masked from 'package:base':
backsolve, forwardsolve
Loading required package: maps
# maps v3.1: updated 'world': all lakes moved to separate new #
# 'lakes' database. Type '?world' or 'news(package="maps")'. #
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:spam':
cbind, rbind
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Mulcom/mulParOpt.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mulParOpt
> ### Title: MulCom Parameters Optimization
> ### Aliases: mulParOpt
> ### Keywords: MulCom
>
> ### ** 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))
MulCom optimization starts
initializing ...
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% done
> mulParOpt(mulcom_perm, mulcom_opt, 1, 0.05)
[1] 1190
t m
2.0 0.2
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.