Example data for package maCorrSample

Description

Example expression data to demonstrate the functionality of the package: two data sources A and B with 30 patients and 1000 genes each, for each of which we have RMA expression values, (logarithmized) MAS5 expression values, and MAS5 absent/present calls.

Correspondingly, we have six data matrices whose name are constructed as dat[A|B].[rma|mas5|amp].

Usage

data(oligodata)

Format

All matrices have genes as rows and samples as columns.

Source

These are small anonymized excerpts from a real breast cancer data set.

See Also

CorrSample, plot.corr.sample

Examples

data(oligodata)
str(datA.rma)
str(datB.rma)
str(datA.mas5)
str(datB.mas5)
str(datA.amp)
str(datB.amp)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(maCorrPlot)
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maCorrPlot/oligodata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: oligodata
> ### Title: Example data for package maCorrSample
> ### Aliases: oligodata datA.rma datB.rma datA.mas5 datB.mas5 datA.amp
> ###   datB.amp
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(oligodata)
> str(datA.rma)
 num [1:1000, 1:30] 4.01 7.57 7.97 6.43 8.24 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:1000] "g1" "g34" "g46" "g50" ...
  ..$ : chr [1:30] "patA1" "patA2" "patA3" "patA4" ...
> str(datB.rma)
 num [1:1000, 1:30] 3.94 3.57 5.64 8.55 7.36 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:1000] "g4" "g12" "g28" "g33" ...
  ..$ : chr [1:30] "patB1" "patB2" "patB3" "patB4" ...
> str(datA.mas5)
 num [1:1000, 1:30] 1.89 4.55 5.03 1.83 5.02 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:1000] "g1" "g34" "g46" "g50" ...
  ..$ : chr [1:30] "patA1" "patA2" "patA3" "patA4" ...
> str(datB.mas5)
 num [1:1000, 1:30] 2.098 -0.0196 1.1275 5.0293 4.2963 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:1000] "g4" "g12" "g28" "g33" ...
  ..$ : chr [1:30] "patB1" "patB2" "patB3" "patB4" ...
> str(datA.amp)
 chr [1:1000, 1:30] "A" "P" "P" "A" "P" "P" "P" "A" "P" ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:1000] "g1" "g34" "g46" "g50" ...
  ..$ : chr [1:30] "patA1" "patA2" "patA3" "patA4" ...
> str(datB.amp)
 chr [1:1000, 1:30] "A" "A" "A" "M" "A" "A" "P" "P" "P" ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:1000] "g4" "g12" "g28" "g33" ...
  ..$ : chr [1:30] "patB1" "patB2" "patB3" "patB4" ...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>