generates a consensus matrix from list of genes

Description

generates a consensus matrix from list of genes

Usage

mulInt(...)

Arguments

Details

mulCAND generates a consensus matrix from list of genes

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(0,0.5, 0.1), vt = seq(1,3, 0.1))

h1_opt <- mulParOpt(mulcom_perm, mulcom_opt, ind = 1, th = 0.05)
h2_opt <- mulParOpt(mulcom_perm, mulcom_opt, ind = 1, th = 0.05)

int <- mulInt(h1_opt, h2_opt)

Results

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/mulInt.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mulInt
> ### Title: generates a consensus matrix from list of genes
> ### Aliases: mulInt
> ### Keywords: MulCom
> 
> ### ** Examples
> 
> data(benchVign)
> mulcom_perm <- mulPerm(Affy, Affy$Groups, 10,2)
> mulcom_opt <- mulOpt(mulcom_perm, vm = seq(0,0.5, 0.1), vt = seq(1,3, 0.1))
MulCom optimization starts
initializing ...
0%  10%  20%  30%  40%  50%  60%  70%  80%  90%  100%   done
> 
> h1_opt <- mulParOpt(mulcom_perm, mulcom_opt, ind = 1, th = 0.05)
[1] 1893
> h2_opt <- mulParOpt(mulcom_perm, mulcom_opt, ind = 1, th = 0.05)
[1] 1893
> 
> int <- mulInt(h1_opt, h2_opt)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>