Accessors and replacement methods for the intensity/PM/MM/BG matrices.

Description

Accessors and replacement methods for the PM/MM/BG matrices.

Usage

intensity(object)
mm(object, subset = NULL, target='core')
pm(object, subset = NULL, target='core')
bg(object, subset = NULL)
mm(object, subset = NULL, target='core')<-value
pm(object, subset = NULL, target='core')<-value
bg(object)<-value

Arguments

Details

For all objects but TilingFeatureSet, these methods will return matrices. In case of TilingFeatureSet objects, the value is a 3-dimensional array (probes x samples x channels).

intensity will return the whole intensity matrix associated to the object. pm, mm, bg will return the respective PM/MM/BG matrix.

When applied to ExonFeatureSet or GeneFeatureSet objects, pm will return the PM matrix at the transcript level ('core' probes) by default. The user should set the target argument accordingly if something else is desired. The valid values are: 'probeset' (Exon and Gene arrays), 'core' (Exon and Gene arrays), 'full' (Exon arrays) and 'extended' (Exon arrays).

The target argument has no effects when used on designs other than Gene and Exon ST.

Examples

if (require(maqcExpression4plex) & require(pd.hg18.60mer.expr)){
xysPath <- system.file("extdata", package="maqcExpression4plex")
xysFiles <- list.xysfiles(xysPath, full.name=TRUE)
ngsExpressionFeatureSet <- read.xysfiles(xysFiles)
pm(ngsExpressionFeatureSet)[1:10,]
}

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 '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.
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> library(oligo)
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

Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/oligo/IntensityMatrix-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mm
> ### Title: Accessors and replacement methods for the intensity/PM/MM/BG
> ###   matrices.
> ### Aliases: mm pm bg intensity intensity,FeatureSet-method
> ###   mm,FeatureSet-method pm,FeatureSet-method bg,FeatureSet-method
> ###   mm,TilingFeatureSet-method pm,TilingFeatureSet-method
> ###   bg,TilingFeatureSet-method intensity<- mm<- pm<- bg<-
> ###   intensity<-,FeatureSet-method mm<-,FeatureSet,ANY,ANY,matrix-method
> ###   pm<-,FeatureSet,ANY,ANY,matrix-method bg<-,FeatureSet,matrix-method
> ###   mm<-,FeatureSet,ANY,ANY,ff_matrix-method
> ###   pm<-,FeatureSet,ANY,ANY,ff_matrix-method
> ###   bg<-,FeatureSet,ff_matrix-method
> ###   mm<-,TilingFeatureSet,ANY,ANY,array-method
> ###   pm<-,TilingFeatureSet,ANY,ANY,array-method
> ###   bg<-,TilingFeatureSet,array-method pm,GenericFeatureSet-method
> ###   pm<-,GenericFeatureSet,ANY,ANY,ff_matrix-method
> ###   pm<-,GenericFeatureSet,ANY,ANY,matrix-method
> ### Keywords: manip
> 
> ### ** Examples
> 
> if (require(maqcExpression4plex) & require(pd.hg18.60mer.expr)){
+ xysPath <- system.file("extdata", package="maqcExpression4plex")
+ xysFiles <- list.xysfiles(xysPath, full.name=TRUE)
+ ngsExpressionFeatureSet <- read.xysfiles(xysFiles)
+ pm(ngsExpressionFeatureSet)[1:10,]
+ }
Loading required package: maqcExpression4plex
/-------------------------------------------
| SAMPLE EXPRESSION DATA - MAQC/ HG18 - NGS |
|-------------------------------------------|
| Data provided by NimbleGen Systems (NGS). |
| This package is meant to be used only for |
| demonstration of BioConductor packages.   |
|-------------------------------------------|
| The contents of this package are provided |
| in good faith and the maintainer does not |
| warrant their accuracy.                   |
-------------------------------------------/
Loading required package: pd.hg18.60mer.expr
Loading required package: RSQLite
Loading required package: DBI
Platform design info loaded.
Checking designs for each XYS file... Done.
Allocating memory... Done.
Reading /home/ddbj/local/lib64/R/library/maqcExpression4plex/extdata/9868701_532.xys.
Reading /home/ddbj/local/lib64/R/library/maqcExpression4plex/extdata/9868901_532.xys.
Reading /home/ddbj/local/lib64/R/library/maqcExpression4plex/extdata/9869001_532.xys.
Reading /home/ddbj/local/lib64/R/library/maqcExpression4plex/extdata/9870301_532.xys.
Reading /home/ddbj/local/lib64/R/library/maqcExpression4plex/extdata/9870401_532.xys.
Reading /home/ddbj/local/lib64/R/library/maqcExpression4plex/extdata/9870601_532.xys.
    9868701_532.xys 9868901_532.xys 9869001_532.xys 9870301_532.xys
398         1476.00         1133.00         1289.56          559.56
399          254.44          263.22          238.56          328.67
400          159.00          185.11          150.78          268.11
401          310.78          301.33          301.78          278.67
402         1332.22         1114.11         1103.11          869.11
403          386.44          509.22          373.33          438.33
404          246.33          326.89          222.33         6179.11
405        32296.00        26510.00        30906.89         2631.44
406          132.78          165.56          139.56          300.89
407          238.56          248.89          216.89          338.33
    9870401_532.xys 9870601_532.xys
398          581.44          560.78
399          285.22          285.89
400          226.56          210.22
401          268.11          260.56
402          809.44          836.67
403          422.44          447.89
404          276.22          275.56
405         2646.89         2607.11
406          301.56          285.33
407          328.89          316.78
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>