Class "aGFFCalc"

Description

Store results of ACME calculations

Objects from the Class

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

Slots

call:

Object of class "call", contains the exact call to do.aGFF.calc, for historical purposes

threshold:

Object of class "numeric", the threshold used in the calculation

cutpoints:

Object of class "numeric", the data value above which probes were considered positive

vals:

Object of class "matrix", equivalent in size to the original data matrix, containing the calculated p-values from the ACME algorithm

annotation:

Object of class "data.frame", currently a copy of the original annotation, possibly reordered in chromosome order

data:

Object of class "matrix", the original data, possibly reordered

samples:

Object of class "data.frame", sample metadata

Extends

Class "aGFF", directly.

Methods

plot

signature(x = "aGFFCalc", ask=FALSE): plot the results of an ACME calculation

print

signature(x = "aGFFCalc"): brief overview of the object

show

signature(object = "aGFFCalc"): brief overview of the object

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

See Also

do.aGFF.calc, aGFF-class

Examples

data(example.agff)
example.agffcalc <- do.aGFF.calc(example.agff,window=1000,thresh=0.9)
example.agffcalc

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 '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(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/aGFFCalc-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: aGFFCalc-class
> ### Title: Class "aGFFCalc"
> ### Aliases: aGFFCalc-class plot,aGFFCalc-method print,aGFFCalc-method
> ###   show,aGFFCalc-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> data(example.agff)
> example.agffcalc <- do.aGFF.calc(example.agff,window=1000,thresh=0.9)
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  > example.agffcalc
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: 0.9 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>