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Last data update: 2014.03.03

R: Wrapper function for effect size or p-value combination...

metaMA

R Documentation

Wrapper function for effect size or p-value combination methods

Description

This is a wrapper function for effect size or p-value combination as implemented in metaMA package.

Usage

metaMA(data, varname, moderated = c("limma", "SMVar", "t")[1], BHth = 0.05, which = c("pval", "ES")[1])

Arguments

`data`	MetaArray object containing gene expression data matrices, clinical data matrices and a vector of data set names. The gene expression data matrices must have equal rownames
`varname`	Character String - name of one column in clinical data matrices to be used as class labels
`moderated`	Character - method to calculate the test statistic (or p-value) inside each study, one of: "limma", "SMVar" and "t"
`BHth`	Numeric - threshold for Benjamini Hochenberg adjusted p-values for selection of significant genes in meta-analysis
`which`	Character - choose `"pval"` for combination of p-values, or `"ES"` for effect sizes

Value

An object of class "metaMA.res". It is a list where:

`Study1`	Vector of indices of differentially expressed genes in study 1. Similar names are given for the other individual studies.
`AllIndStudies`	Vector of indices of differentially expressed genes found by at least one of the individual studies.
`Meta`	Vector of indices of differentially expressed genes in the meta-analysis.
`TestStatistic`	Vector with test statistics for differential expression in the meta-analysis.

Author(s)

Ivana Ihnatova

References

Marot, G., Foulley, J.-L., Mayer, C.-D., Jaffrezic, F. Moderated effect size and p-value combinations for microarray meta-analyses.

Examples

data(ColonData)
pv<-metaMA(ColonData, "MSI", moderated = "t")

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/metaMA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: metaMA
> ### Title: Wrapper function for effect size or p-value combination methods
> ### Aliases: metaMA metaMA.res
> ### Keywords: univar
> 
> ### ** Examples
> 
> data(ColonData)
> pv<-metaMA(ColonData, "MSI", moderated = "t")
    DE    IDD   Loss    IDR    IRR 
215.00  43.00  20.00  20.00  10.42 
>   
> 
> 
> 
> 
> dev.off()
null device 
          1 
>