Function to do convert list to matrix

Description

Function converts list (output from pvalcombination, EScombination, metaMA) to matrix. )

Usage

metalist.to.matrix(list, genenames = NULL)

Arguments

Value

Matrix. Last columns contains test statistics (last slot from metalist). Other columns are binary vector indicating that the index of the gene was present in other slots of metalist.

Author(s)

Ivana Ihnatova

Examples

data(Singhdata)
pvalt<-pvalcombination(
  esets=Singhdata$esets, 
  classes=Singhdata$classes, 
  moderated = "t", BHth = 0.01)
xx<-metalist.to.matrix(pvalt,Singhdata$geneNames)

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(MAMA)
Loading required package: genefilter
Loading required package: metaMA

Attaching package: 'metaMA'

The following object is masked from 'package:genefilter':

    rowVars

Loading required package: xtable
Loading required package: multtest
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: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

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: gtools
Loading required package: grid
Loading required package: GeneMeta

Attaching package: 'MAMA'

The following objects are masked from 'package:GeneMeta':

    multExpFDR, zScoreFDR, zScorePermuted, zScores

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MAMA/metalist.to.matrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: metalist.to.matrix
> ### Title: Function to do convert list to matrix
> ### Aliases: metalist.to.matrix
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(Singhdata)
> pvalt<-pvalcombination(
+   esets=Singhdata$esets, 
+   classes=Singhdata$classes, 
+   moderated = "t", BHth = 0.01)
     DE     IDD    Loss     IDR     IRR 
1379.00 1374.00    0.00   99.64    0.00 
> xx<-metalist.to.matrix(pvalt,Singhdata$geneNames)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>