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Last data update: 2014.03.03

R: Wrapper function for METRADISC method

METRADISC

R Documentation

Wrapper function for METRADISC method

Description

This is a wrapper function for meta-analytical method called METRADISC that perform all steps of the analysis and return all the outputs in one line.

Usage

METRADISC(data, varname, nperm = 1000)

Arguments

`data`	MetaArray object
`varname`	Character String - name of one column in clinical data matrices to be used as class labels
`nperm`	Number of permutations for Monte Carlo permutation test, at least 1000 is suggested

Value

An object of class METRADISC.res containing

`ranks`	Ranks of the genes in each dataset
`RQ`	Average rank (R) and measure of heterogeneity (Q) for each gene
`MCtest`	Four p-values (for low and high R and low and high Q) for each gene as provided after Monte Carlo permutation test

Author(s)

Ivana Ihnatova

References

Zintzaras, E., Ioannidis, J.P.A 2008 Meta-analysis for ranked discovery datasets: Theoretical framework and empirical demonstration for microarrays, Computational Biology and Chemistry 32, 39-47

Examples

data(ColonData)
m <- METRADISC(ColonData, "MSI", 5)

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(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/METRADISC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: METRADISC
> ### Title: Wrapper function for METRADISC method
> ### Aliases: METRADISC.res METRADISC
> ### Keywords: univar
> 
> ### ** Examples
> 
> data(ColonData)
> m <- METRADISC(ColonData, "MSI", 5)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>