Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/utility03282012.r
When multiple probes (or probe sets) matched to an identical gene symbol, these functions are used to match them into a single gene symbol.
1 2 | Match.gene(x, pool.replicate = c("average", "IQR"))
MetaDE.match(x,pool.replicate = c("average", "IQR"))
|
x |
a list of studies. Each study is a list with components:
|
pool.replicate |
a character to specify the method to match multiple probeIds to a single gene symbol. see "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.
A list with components:
data |
a list of gene expression datasets. |
l |
a list of labels. |
Jia Li and Xingbin Wang
Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S (eds.): Bioinformatics and Computational Biology Solutions Using R and Bioconductor: Springer; 2005.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | #================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")
|
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
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Vignettes contain introductory material; view with
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'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
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