ES.GeneMeta: Wrapper function for combining the effect size as implemented...

In MAMA: Meta-Analysis of MicroArray

Description

This is a wrapper function for meta-analytical method implemented in GeneMeta package

Usage

ES.GeneMeta(data, varname, useREM = TRUE, CombineExp = 1:length(esets), nperm = 1000)

Arguments

data	MetaArray object
varname	Character String - name of one column in clinical data matrices to be used as class labels
useREM	Logical - indicating whethet Random Effect Model (REM) shuld be used, if FALSE then Fixed Effect Model is applied
CombineExp	A numeric vector - which experiments should be combined, all experiments are set as default
nperm	Number of permutations to calculate FDR

Value

An object of class ES.GeneMeta.res

theScores	Ouput from function zScores
ScoresFDR	Output from function zScoreFDR

Author(s)

Ivana Ihnatova

References

Choi et al, Combining multiple microarray studies and modeling interstudy variation. Bioinformatics, 2003, i84-i90.

See Also

zScores, zScoreFDR

Examples

data(ColonData)
es<- ES.GeneMeta(ColonData, "MSI", nperm = 10)

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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

MAMA documentation built on Jan. 15, 2017, 3:05 p.m.