mergedata: Function to merge data from MetaArray object

In MAMA: Meta-Analysis of MicroArray

Description

Function merges the data stored in MetaArray object. It binds expression data matrices into one gene expression data matrix. It creates one binary vector of class labels of the samples and one numeric vector of orgin of the samples.

Usage

mergedata(x, varname)

Arguments

x	MetaArray objec
varname	character String specifying the column of clinical data to be used in vector of class labels of the samples

Value

A list with three slots

dat	Gene expression data matrix, rows refer to genes/probes and columns to samples
cl	Binary vector of class labels of the samples
origin	Numeric vector describing the origin of the samples. Same number refers to samples from one study

Author(s)

Ivana Ihnatova

Examples

data(Singhdata)

cl1<-as.data.frame(Singhdata$classes[[1]])
names(cl1)<-"classlab"
cl2<-as.data.frame(Singhdata$classes[[2]])
names(cl2)<-"classlab"
cl3<-as.data.frame(Singhdata$classes[[3]])
names(cl3)<-"classlab"
rownames(Singhdata$esets[[1]])<-Singhdata$geneNames
rownames(Singhdata$esets[[2]])<-Singhdata$geneNames
rownames(Singhdata$esets[[3]])<-Singhdata$geneNames

data<-new("MetaArray", GEDM=list(Singhdata$esets[[1]], Singhdata$esets[[2]], Singhdata$esets[[3]]),
clinical=list(cl1, cl2, cl3), datanames=c("dataset1", "dataset2", "dataset3"))

merged.data<-mergedata(data,"classlab")
summary(merged.data)

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, cbind, colMeans, colSums, 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, 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

       Length Class      Mode   
dat    60     data.frame list   
cl     60     -none-     numeric
origin 60     -none-     numeric

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