Method specifies the model used to generate coefficients. At this time only linear regression, logistic regression, and Cox hazard rates are implemented.
outcome, outcome2
The format for the outcome variable depends on the model used. For linear regression, outcome should be a continous response variable, for logistic regression, it should be a binary response variable, and for Cox hazard rates it should be time of event. Outcome 2 is currently used only in the calculation of hazard rates, and should be a binary variable indicating censoring status for each subject.
If outcome is a vector of length equal to number of studies, then each element represents the column in the ExpressionSet phenoData slot for that study. If outcome is a list, then each list element should have actual outcome data for the corresponding study.
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> library(MergeMaid)
Loading required package: survival
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: MASS
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MergeMaid/modelOutcome.Rd_%03d_medium.png", width=480, height=480)
> ### Name: modelOutcome
> ### Title: Compare regression coefficients across studies
> ### Aliases: modelOutcome
> ### Keywords: models
>
> ### ** Examples
>
> if(require(Biobase) & require(MASS) & require(survival)){
+ data(mergeData)
+ merged <- mergeExprs(sample1,sample2,sample3)
+
+ log.coeff <- modelOutcome(merged,outcome=c(1,1,1),method="logistic")
+ plot(coeff(log.coeff))
+
+ linear.coeff <- modelOutcome(merged[1:2],outcome=c(3,3),method="linear")
+ plot(zscore(linear.coeff),xlab="study 1",ylab="study 2")
+
+ event1<-rbinom(100,1,.5)
+ event2<-rbinom(50,1,.5)
+ event3<-rbinom(70,1,.5)
+
+ out1<-rnorm(100,5,1)
+ out2<-rnorm(50,5,1)
+ out3<-rnorm(70,5,1)
+
+ out<-list(out1,out2,out3)
+ even<-list(event1,event2,event3)
+
+ cox.coeff<-modelOutcome(merged,outcome2=even,outcome=out,method="cox")
+ plot(coeff(cox.coeff))
+
+ }
NULL
>
>
>
>
>
> dev.off()
null device
1
>