Class mergeCoeff, a class for storing regression coefficients.

Description

This is the class representation for output from regression coefficient calculations

Slots

coeff

Object of class matrix, A matrix storing default coefficients.

coeff.std

Object of class matrix, A matrix storing standardized coefficients.

zscore

Object of class matrix, A matrix storing zscores.

Methods

Class-specific methods:

coeff (mergeCoeff)

Accessor function for the coeff slot.

coeff<- (mergeCoeff)

Replacement function for the coeff slot.

stdcoeff (mergeCoeff)

Accessor function for the coeff.std slot.

stdcoeff<- (mergeCoeff)

Replacement function for the coeff.std slot.

zscore (mergeCoeff)

Accessor function for the zscore slot.

zscore<- (mergeCoeff)

Replacement function for the zscore slot.

Standard generic methods:

plot (list)

This method is not formally defined for mergeCoeff objects but for a matrix. This function would typically be called with the following syntax, plot(coeff(mergeCoeff)).The result is pairwise scatterplots of the columns of the selected matrix. If there are two studies, this is a single scatterplot.

See Also

mergeExprs,modelOutcome, mergeExpressionSet-class

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))
  plot(stdcoeff(log.coeff),pch=4,labels=c("study A","study B","study C"),col=3)

  linear.coeff  <- modelOutcome(merged[1:2],outcome=c(3,3),method="linear")
  plot(zscore(linear.coeff))
  plot(zscore(linear.coeff),xlab="study A",ylab="study B",col=2)
  }

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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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/class.mergeCoeff.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mergeCoeff
> ### Title: Class mergeCoeff, a class for storing regression coefficients.
> ### Aliases: mergeCoeff-class mergeCoeff check.length coeff coeff<-
> ###   stdcoeff stdcoeff<- zscore zscore<- coeff,mergeCoeff-method
> ###   stdcoeff,mergeCoeff-method zscore,mergeCoeff-method
> ###   coeff<-,mergeCoeff-method stdcoeff<-,mergeCoeff-method
> ###   zscore<-,mergeCoeff-method mergeCoeff
> ### Keywords: classes
> 
> ### ** 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))
+   plot(stdcoeff(log.coeff),pch=4,labels=c("study A","study B","study C"),col=3)
+ 
+   linear.coeff  <- modelOutcome(merged[1:2],outcome=c(3,3),method="linear")
+   plot(zscore(linear.coeff))
+   plot(zscore(linear.coeff),xlab="study A",ylab="study B",col=2)
+   }
NULL
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>