Methods for class CopyNumberSet.

Description

Accessors and CopyNumberSet

Usage

copyNumber(object, ...)
cnConfidence(object)
copyNumber(object) <- value
cnConfidence(object) <- value

Arguments

Value

copyNumber returns a matrix of copy number estimates or relative copy number estimates. Since the copy number estimates are stored as integers (copy number * 100), the matrix returned by the copyNumber accessor will need to be divided by a factor of 100 to transform the measurements back to the original copy number scale.

cnConfidence returns a matrix of confidence scores for the copy number estimates. These are also represented as integers and will require a back-transformation to the original scale.

Examples

	library(Biobase)
	data(locusLevelData)
	path <- system.file("extdata", package="oligoClasses")
	fd <- readRDS(file.path(path, "genomeAnnotatedDataFrameExample.rds"))
	## the following command creates an 'oligoSnpSet' object, storing
	## an integer representation of the log2 copy number in the 'copyNumber' element
	## of the assayData.  Genotype calls and genotype confidence scores are also stored
	## in the assayData.
	oligoSet <- new("oligoSnpSet",
			copyNumber=integerMatrix(log2(locusLevelData[["copynumber"]]/100), 100),
			call=locusLevelData[["genotypes"]],
			callProbability=integerMatrix(locusLevelData[["crlmmConfidence"]], 1),
			annotation=locusLevelData[["platform"]],
			featureData=fd,
			genome="hg19")

	## There are several accessors for the oligoSnpSet class.
	icn <- copyNumber(oligoSet)
	range(icn) ## integer scale
	lcn <- icn/100
	range(lcn) ## log2 copy number

	## confidence scores for the genotypes are also represented on an integer scale
	ipr <- snpCallProbability(oligoSet)
	range(ipr) ## integer scale

	## for genotype confidence scores, the helper function i2p
	## converts back to a probability scale
	pr <- i2p(ipr)
	range(pr)

	## The helper function confs is a shortcut, extracting the
	## integer-based confidence scores and transforming to the
	## probability scale
	pr2 <- confs(oligoSet)
	all.equal(pr, pr2)

	## To extract information on the annotation of the SNPs, one can use
	position(oligoSet)
	chromosome(oligoSet)
	## the position and chromosome coordinates were extracted from build hg19
	genomeBuild(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/CopyNumberSet-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CopyNumberSet-methods
> ### Title: Methods for class CopyNumberSet.
> ### Aliases: CopyNumberSet-methods copyNumber copyNumber<- cnConfidence
> ###   cnConfidence<-
> ### Keywords: methods manip
> 
> ### ** Examples
> 
> 	library(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")'.

> 	data(locusLevelData)
> 	path <- system.file("extdata", package="oligoClasses")
> 	fd <- readRDS(file.path(path, "genomeAnnotatedDataFrameExample.rds"))
> 	## the following command creates an 'oligoSnpSet' object, storing
> 	## an integer representation of the log2 copy number in the 'copyNumber' element
> 	## of the assayData.  Genotype calls and genotype confidence scores are also stored
> 	## in the assayData.
> 	oligoSet <- new("oligoSnpSet",
+ 			copyNumber=integerMatrix(log2(locusLevelData[["copynumber"]]/100), 100),
+ 			call=locusLevelData[["genotypes"]],
+ 			callProbability=integerMatrix(locusLevelData[["crlmmConfidence"]], 1),
+ 			annotation=locusLevelData[["platform"]],
+ 			featureData=fd,
+ 			genome="hg19")
> 
> 	## There are several accessors for the oligoSnpSet class.
> 	icn <- copyNumber(oligoSet)
> 	range(icn) ## integer scale
[1] -108  317
> 	lcn <- icn/100
> 	range(lcn) ## log2 copy number
[1] -1.08  3.17
> 
> 	## confidence scores for the genotypes are also represented on an integer scale
> 	ipr <- snpCallProbability(oligoSet)
> 	range(ipr) ## integer scale
[1]  976 7598
> 
> 	## for genotype confidence scores, the helper function i2p
> 	## converts back to a probability scale
> 	pr <- i2p(ipr)
> 	range(pr)
[1] 0.6231847 0.9994985
> 
> 	## The helper function confs is a shortcut, extracting the
> 	## integer-based confidence scores and transforming to the
> 	## probability scale
> 	pr2 <- confs(oligoSet)
> 	all.equal(pr, pr2)
[1] TRUE
> 
> 	## To extract information on the annotation of the SNPs, one can use
> 	position(oligoSet)
   [1]    846864   2234251   2925539   2936870   2951244   2951834   2973576
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 [106]   7639308   7689389   7761001   7769478   7770132   7801288   7911099
 [113]   7929819   7930554   7938648   7961206   7961801   7961855   7999602
 [120]   8079301   8100140   8242487   8372536   8413839   8468372   8469337
 [127]   8495590   8495945   8598005   8598127   8629380   8810341   9285721
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[1051]  52953766  52955458  53047593  53104038  53189816  53267280  53301876
[1058]  53361928  53414766  53458199  53460091  53461264  53523904  53526104
[1065]  53526247  53569399  53575012  53590630  53621345  53621628  53622016
[1072]  53622093  53624435  53628815  53757935  53771202  54038001  54038536
[1079]  54053788  54198206  54198318  54198562  54201278  54216654  54269087
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[1156]  55979499  55984309  55984513  55991073  55992810  56009470  56011258
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[1191]  56321789  56326293  56328238  56328941  56333648  56335942  56344912
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