Class "ACMECalcSet"

Description

A subclass of ACMESet that can also store the parameters and results of an ACME calculation

Objects from the Class

Objects can be created by calls of the form new("ACMECalcSet", assayData, phenoData, featureData, experimentData, annotation, cutpoints, threshold, exprs, vals, ...). In addition to the constraints defined by ACMESet, this class can also hold the results (in the assayDataElement vals) and the threshold and cutpoints from an ACME do.aGFF.calc run

Slots

cutpoints:

Object of class "numeric" The values of the cutpoints used in an analysis by do.aGFF.calc, one per sample.

threshold:

Object of class "numeric" The threshold used in an analysis.

assayData:

Object of class "AssayData". See ExpressionSet for details.

phenoData:

Object of class "AnnotatedDataFrame" See ExpressionSet for details.

featureData:

Object of class "AnnotatedDataFrame" See ExpressionSet for details.

experimentData:

Object of class "MIAME" See ExpressionSet for details.

annotation:

Object of class "character" See ExpressionSet for details.

.__classVersion__:

Object of class "Versions" See ExpressionSet for details.

Extends

Class "ACMESet", directly. Class "ExpressionSet", by class "ACMESet", distance 2. Class "eSet", by class "ACMESet", distance 3. Class "VersionedBiobase", by class "ACMESet", distance 4. Class "Versioned", by class "ACMESet", distance 5.

Methods

cutpoints

signature(x = "ACMECalcSet"): A simple getter for the cutpoints.

plot

signature(x = "ACMECalcSet"): A convenience plotting method that also takes sample and chrom

show

signature(object = "ACMECalcSet"): A show method

threshold

signature(x = "ACMECalcSet"): A simple getter for the threshold

vals

signature(x = "ACMECalcSet"): an accessor for the p-values from a run of do.aGFF.calc. Returns a matrix with samples in columns and probes in rows.

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

See Also

ACMESet

Examples

showClass("ACMECalcSet")
data(example.agff)
b <- do.aGFF.calc(example.agff,thresh=0.95,window=1000)
b
head(vals(b))
threshold(b)
cutpoints(b)

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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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(ACME)
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ACME/ACMECalcSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ACMECalcSet-class
> ### Title: Class "ACMECalcSet"
> ### Aliases: ACMECalcSet-class cutpoints,ACMECalcSet-method
> ###   plot,ACMECalcSet-method show,ACMECalcSet-method
> ###   threshold,ACMECalcSet-method vals,ACMECalcSet-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("ACMECalcSet")
Class "ACMECalcSet" [package "ACME"]

Slots:
                                                               
Name:           cutpoints          threshold     experimentData
Class:            numeric            numeric              MIAME
                                                               
Name:           assayData          phenoData        featureData
Class:          AssayData AnnotatedDataFrame AnnotatedDataFrame
                                                               
Name:          annotation       protocolData  .__classVersion__
Class:          character AnnotatedDataFrame           Versions

Extends: 
Class "ACMESet", directly
Class "ExpressionSet", by class "ACMESet", distance 2
Class "eSet", by class "ACMESet", distance 3
Class "VersionedBiobase", by class "ACMESet", distance 4
Class "Versioned", by class "ACMESet", distance 5
> data(example.agff)
> b <- do.aGFF.calc(example.agff,thresh=0.95,window=1000)
Working on sample 1
Working on chromosome: 
chr1  chr10  chr11  chr12  chr13  chr14  chr15  chr16  chr17  chr18  chr19  chr2  chr20  chr21  chr22  chr3  chr4  chr5  chr6  chr7  chr8  chr9  chrX  Working on sample 2
Working on chromosome: 
chr1  chr10  chr11  chr12  chr13  chr14  chr15  chr16  chr17  chr18  chr19  chr2  chr20  chr21  chr22  chr3  chr4  chr5  chr6  chr7  chr8  chr9  chrX  > b
ACMECalcSet (storageMode: lockedEnvironment)
assayData: 190181 features, 2 samples 
  element names: exprs, vals 
protocolData: none
phenoData
  sampleNames: testsamp1 testsamp2
  varLabels: fullfnames
  varMetadata: labelDescription
featureData
  featureNames: 74065 74066 ... 103913 (190181 total)
  fvarLabels: chromosome source ... comment (8 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
Threshold: 0.95 
> head(vals(b))
      testsamp1 testsamp2
74065 0.6463563 0.6463563
74066 0.6463563 0.6463563
74067 0.6079601 0.6079601
74068 0.5741505 0.5741505
74069 0.5164139 0.5164139
74070 0.5438677 0.5438677
> threshold(b)
[1] 0.95
> cutpoints(b)
testsamp1 testsamp2 
0.4841682 0.3770896 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>