Class "proboStruct"

Description

structure for managing proboscis plot data

Objects from the Class

Objects can be created by calls of the form new("proboStruct", ...).

Slots

.Data:

Object of class "list" ~~

call:

Object of class "call" ~~

Extends

Class "list", from data part. Class "vector", by class "list", distance 2. Class AssayData-class, by class "list", distance 2.

Methods

plot

Note

The proboscis plot shows how the probability of self-consistent monotone titration (SCMT) varies with the spiked difference in concentrations of two mRNA preparations in an MAQC dataset.

Author(s)

V Carey <stvjc@channing.harvard.edu>

References

For Figure 2 of Shippy et al., Using RNA sample titrations... (Nat Biotech, 24(9):1123-1131, Sep 2006)

Examples

data(afxsubRMAES)
NN1 = proboscis(afxsubRMAES)
plot(NN1)
showClass("proboStruct")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(MAQCsubset)
Loading required package: affy
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

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: lumi
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'lumi'

The following objects are masked from 'package:affy':

    MAplot, plotDensity

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MAQCsubset/proboStruct-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: proboStruct-class
> ### Title: Class "proboStruct"
> ### Aliases: proboStruct-class lines,proboStruct-method
> ###   plot,proboStruct-method plot,proboStruct,ANY-method
> ###   show,proboStruct-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> data(afxsubRMAES)
> NN1 = proboscis(afxsubRMAES)
Loading required package: genefilter
> plot(NN1)
> showClass("proboStruct")
Class "proboStruct" [package "MAQCsubset"]

Slots:
                  
Name:  .Data  call
Class:  list  call

Extends: 
Class "list", from data part
Class "vector", by class "list", distance 2
Class "AssayData", by class "list", distance 2
Class "vectorORfactor", by class "list", distance 3
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>