MetaDE.match: Match the probeIds to gene symbol

In MetaDE: MetaDE: Microarray meta-analysis for differentially expressed gene detection

Description

When multiple probes (or probe sets) matched to an identical gene symbol, these functions are used to match them into a single gene symbol.

Usage

Match.gene(x, pool.replicate = c("average", "IQR"))
MetaDE.match(x,pool.replicate = c("average", "IQR"))

Arguments

x	a list of studies. Each study is a list with components: x: the gene expression matrix. y: the outcome. censoring.status: the censoring status. This only for survival data. symbol: the gene symbols.
pool.replicate	a character to specify the method to match multiple probeIds to a single gene symbol. see "Details".

Details

To be able to be combined, Probes (or probe sets) in each study need to be matched to official gene symbols. When multiple probes (or probe sets) matched to an identical gene symbol, the probe that presented the greatest inter-quartile range (IQR) was selected to represent the target gene symbol. Larger IQR represents greater variability (and thus greater information content) in the data and this probe matching method has been recommended in Bioconductor. Another matching method is to take average across genes.

Function, Match.gene,is used to perform matching on a single study; MetaDE.match is used to apply on multiple study sets.

Value

A list with components:

data	a list of gene expression datasets.
l	a list of labels.

Author(s)

Jia Li and Xingbin Wang

References

Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S (eds.): Bioinformatics and Computational Biology Solutions Using R and Bioconductor: Springer; 2005.

See Also

MetaDE.Read, MetaDE.filter

Examples

#================example simulate data sets===============================================#
label1<-rep(0:1,each=5)
label2<-rep(0:1,each=5)
time1=c(4,3,1,1,2,2,3,10,5,4)
event1=c(1,1,1,0,1,1,0,0,0,1)
exp1<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,2),20,5))
exp2<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,1.5),20,5))
rownames(exp1)<-paste("g1",1:20,sep="_")
rownames(exp2)<-paste("g2",1:20,sep="_")
symbol1<-sample(c("SST","VGF","CNP"),20,replace=TRUE)
symbol2<-sample(c("SST","VGF","CNP"),20,replace=TRUE)
study1<-cbind(c(NA,NA,symbol1),rbind(rbind(time1,event1),exp1))
study2<-cbind(c(NA,symbol2),rbind(label2,exp2))
setwd(tempdir())
write.table(study1,"study1.txt",sep="\t")
write.table(study2,"study2.txt",sep="\t")
mydata<-MetaDE.Read(c("study1","study2"),via="txt",skip=c(2,1),log=FALSE)

#----------------------Test MetaDE.match--------------------------------------------------#
mydata.matched2<-MetaDE.match(mydata,"IQR")

Example output

Loading required package: survival
Loading required package: impute
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: combinat

Attaching package: 'combinat'

The following object is masked from 'package:utils':

    combn

Loading required package: tools

MetaDE documentation built on May 29, 2017, 9 a.m.