Class "RTCA"

Description

RTCA object

Objects from the Class

Objects can be created by calls of the form new("RTCA", assayData, phenoData, featureData, experimentData, annotation, exprs, ...). However, it is more common to be constructed by parseRTCA function by reading in RTCA output data directly.

Slots

expID:

Object of class "character", experiment ID

timeline:

Object of class "RTCAtimeline", recording action track along the time line

assayData:

Object of class "AssayData", assay data inherited from ExpressionSet-class

phenoData:

Object of class "AnnotatedDataFrame", pheno data of the assay, annotating the wells

featureData:

Object of class "AnnotatedDataFrame", feature data of the assay, preserved for time-line recording by the package

experimentData:

Object of class "MIAME", idle

annotation:

Object of class "character", idle

.__classVersion__:

Object of class "Versions",idle

Extends

Class ExpressionSet-class, directly. Class eSet-class, by class "ExpressionSet", distance 2. Class VersionedBiobase-class, by class "ExpressionSet", distance 3. Class Versioned-class, by class "ExpressionSet", distance 4.

Methods

addAction

signature(object = "RTCA", time = "numeric", action = "character"): add action at the specified time, passed to the RTCAtimeline slot

getAction

signature(object = "RTCA", time = "numeric"): get action at the specified time, passed to the RTCAtimeline slot

plotRTCA

signature(x = "RTCA"): plot RTCA

rmAction

signature(object = "RTCA", time = "numeric"): remove action at the specified time, passed to the RTCAtimeline slot

show

signature(object = "RTCA"): print method

expID

codesignature(object = "RTCA"): get Experiment ID

expID<-

codesignature(object = "RTCA", value = "ANY"): set Experiment ID

time

signature(x = "RTCA"): deprecated

timeline

signature(object = "RTCA"): get the RTCAtimeline slot

timeline<-

signature(object = "RTCA"): assign the RTCAtimeline slot

timepoints

signature(object = "RTCA"): get the recording time points in a vector

timepoints<-

signature(object = "RTCA"): assign the recording time points

updateAction

signature(object = "RTCA", time = "numeric", action = "character"): update the action at the specified time, passed to the RTCAtimeline slot

plot

signature(x = "RTCA", y): plot the RTCA running plot with matplot. y is interpretated as the indices of the columns to be plotted, and will be expanded to all the columns in case it is missing.

Author(s)

Jitao David Zhang jitao_david.zhang@roche.com

References

1

https://www.roche-applied-science.com/sis/xcelligence/index.jsp?id=xcect_000000 introduces xCelligence system.

2

http://www.roche-applied-science.com/proddata/gpip/3_8_9_1_1_1.html for brief introduction into RTCA

Examples

new("RTCA", expID="testExp01")

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RTCA)
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: RColorBrewer
Loading required package: gtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RTCA/RTCA-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RTCA-class
> ### Title: Class "RTCA"
> ### Aliases: RTCA-class addAction,RTCA,numeric,character-method
> ###   derivativeTransform,RTCA-method getAction,RTCA,numeric-method
> ###   interpolationTransform,RTCA-method plotRTCA,RTCA-method
> ###   ratioTransform,RTCA-method rgrTransform,RTCA-method
> ###   rmAction,RTCA,numeric-method RTCAtimeline,RTCA-method
> ###   RTCAtimeline<-,RTCA-method show,RTCA-method
> ###   smoothTransform,RTCA,missing-method smoothTransform,RTCA,ANY-method
> ###   time,RTCA-method expID expID,RTCA-method expID<- expID<-,RTCA-method
> ###   timeline timeline,RTCA-method timeline<- timeline<-,RTCA-method
> ###   timepoints timepoints,RTCA-method timepoints<-
> ###   timepoints<-,RTCA-method updateAction,RTCA,numeric,character-method
> ###   plot,RTCA-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> new("RTCA", expID="testExp01")
Experiment ID: testExp01 
RTCAtimeline
================================================
 time action
    0  start
================================================
Time unit: hour 
RTCA-run start time: 2016-07-02 23:50:56 

ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 0 samples 
  element names: exprs 
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>