fold.change: Function to do compute fold change between two groups

In MAMA: Meta-Analysis of MicroArray

Description

Function computes fold change between two groups of log2-transformed data

Usage

fold.change(x, varname)

Arguments

x	MetaArray object
varname	Character String specifying which column of clinical data matrices should be used as class labels. Column of this name must be present in each clinical data matrix.

Value

Data frame of fold changes, each column refer to one study and row to genes.

Author(s)

Ivana Ihnatova

Examples

#data preparation
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

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

#fold change
fch<-fold.change(dataset, "classlab")
head(fch)

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

            dataset1     dataset2    dataset3
100_g_at  -0.1211077  0.009699873  0.04517787
1000_at   -0.2410768 -0.208688496 -0.07539162
1001_at   -0.2767953  0.011159164  0.04575200
1002_f_at -0.3073153 -0.045269380 -0.09558148
1003_s_at -0.3465770 -0.026529212 -0.15770542
1004_at   -0.1971677 -0.125110704 -0.08055335

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