An example instance of oligoSnpSet class

Description

An example instance of the oligoSnpSet class

Usage

data(oligoSetExample)

Source

Created from the simulated locusLevelData provided in this package.

See Also

locusLevelData

Examples

	## Not run: 
		## 'oligoSetExample' created by the following
		data(locusLevelData)
		oligoSet <- new("oligoSnpSet",
				copyNumber=integerMatrix(log2(locusLevelData[["copynumber"]]/100), 100),
				call=locusLevelData[["genotypes"]],
				callProbability=locusLevelData[["crlmmConfidence"]],
				annotation=locusLevelData[["platform"]],
				genome="hg19")
		oligoSet <- oligoSet[!is.na(chromosome(oligoSet)), ]
		oligoSet <- oligoSet[chromosome(oligoSet) < 3, ]
	
## End(Not run)
	data(oligoSetExample)
	oligoSet

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(oligoClasses)
Welcome to oligoClasses version 1.34.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/oligoClasses/oligoSetExample.Rd_%03d_medium.png", width=480, height=480)
> ### Name: oligoSet
> ### Title: An example instance of oligoSnpSet class
> ### Aliases: oligoSet
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 	## Not run: 
> ##D 		## 'oligoSetExample' created by the following
> ##D 		data(locusLevelData)
> ##D 		oligoSet <- new("oligoSnpSet",
> ##D 				copyNumber=integerMatrix(log2(locusLevelData[["copynumber"]]/100), 100),
> ##D 				call=locusLevelData[["genotypes"]],
> ##D 				callProbability=locusLevelData[["crlmmConfidence"]],
> ##D 				annotation=locusLevelData[["platform"]],
> ##D 				genome="hg19")
> ##D 		oligoSet <- oligoSet[!is.na(chromosome(oligoSet)), ]
> ##D 		oligoSet <- oligoSet[chromosome(oligoSet) < 3, ]
> ##D 	
> ## End(Not run)
> 	data(oligoSetExample)
> 	oligoSet
oligoSnpSet (storageMode: lockedEnvironment)
assayData: 9249 features, 1 samples 
  element names: call, callProbability, cnConfidence, copyNumber 
protocolData: none
phenoData: none
featureData
  featureNames: SNP_A-1677174 SNP_A-1718890 ... SNP_A-1724680 (9249
    total)
  fvarLabels: isSnp position chromosome
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: pd.mapping50k.hind240,pd.mapping50k.xba240 
genome:  hg19 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>