Class mergeCor, a class for storing data relevant to integrative correlation coefficients.

Description

This is the class representation for integrative correlation coefficients.

Details

If 'n' is the number of studies then for i < j <= n, the pairwise correlation of correlations for studies i and j is stored in column ((i-1)*(n-1)-(i-2)*(i-1)/2 + j-i) of the pairwise.cors slot.

Slots

pairwise.cors

Object of class matrix. Each column contains correlation of correlation score for genes in a pair of study.

maxcors

Object of class vector. Each slot represents maximal canonical correlation (pairwise canonical correlations) for each pair of studies.

notes

Object of class vector. Each slot contains notes for each study.

Methods

Class-specific methods:

cors(mergeCor)

Accessor function for the cors slot.

pairs.cors( mergeCor)

Accessor function for the pairwise.cors slot

integrate.cors(mergeCor)

Accessor function, returns integrative correlation (average pairwise correlation of correlations) for each gene. If adjust is TRUE, returns the integrate correlation devided by the correponding canonical correlation, and the default value is FALSE.

maxcors(mergeCor)

Accessor function, returns maximal canonical correlation (pairwise canonical correlations) for each pair of studies.

Standard generic methods:

notes (mergeCor)

An accessor function for the notes slot.

hist(mergeCor,...)

Draw histograms of integrative correlation, here we use the approximate method to calculate the integrative correlation.

See Also

mergeCor-class,intCor,modelOutcome, mergeExpressionSet-class

Examples

  if(require(Biobase) & require(MASS)){
  data(mergeData)
  merged  <- mergeExprs(sample1,sample2,sample3)
  intcor3  <-intCor(merged,method="pearson")
  plot(merged)
  intcor2  <-intCor(merged[1:2],exact=FALSE)
  plot(merged,pch=4,col=5)

  pairwise.cors(intcor3)
  integrative.cors(intcor3)
  integrative.cors(intcor2)["Hs.12101"]
  maxcors(intcor2)
  }

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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.mergeCor.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mergeCor
> ### Title: Class mergeCor, a class for storing data relevant to integrative
> ###   correlation coefficients.
> ### Aliases: mergeCor-class mergeCor pairwise.cors integrative.cors
> ###   pairwise.cors,mergeCor-method integrative.cors,mergeCor-method
> ###   maxcors,mergeCor-method hist,mergeCor-method plot,list-method
> ###   notes,mergeCor-method hist plot maxcors
> ### Keywords: classes
> 
> ### ** Examples
> 
>   if(require(Biobase) & require(MASS)){
+   data(mergeData)
+   merged  <- mergeExprs(sample1,sample2,sample3)
+   intcor3  <-intCor(merged,method="pearson")
+   plot(merged)
+   intcor2  <-intCor(merged[1:2],exact=FALSE)
+   plot(merged,pch=4,col=5)
+ 
+   pairwise.cors(intcor3)
+   integrative.cors(intcor3)
+   integrative.cors(intcor2)["Hs.12101"]
+   maxcors(intcor2)
+   }
[1] 1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>