M-methods

Description

Extract raw methylated probe intensity from an object of RnBeadRawSet class.

Usage

## S4 method for signature 'RnBeadRawSet'
M(object, row.names = FALSE)

Arguments

Value

matrix of the methylated probe intensities

Examples

library(RnBeads.hg19)
data(small.example.object)
M.intensity<-M(rnb.set.example)
head(M.intensity)
 

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(RnBeads)
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: 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: GenomicRanges
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: MASS
Loading required package: RColorBrewer
Loading required package: cluster
Loading required package: ff
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit

Attaching package: 'bit'

The following object is masked from 'package:base':

    xor

Attaching package ff
- getOption("fftempdir")=="/tmp/Rtmp4EUmjW"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: 'ff'

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

    clone, clone.default, clone.list

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

    write.csv, write.csv2

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

    is.factor, is.ordered

Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following object is masked from 'package:stats4':

    mle

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

    backsolve, forwardsolve

Loading required package: maps

 # maps v3.1: updated 'world': all lakes moved to separate new #
 # 'lakes' database. Type '?world' or 'news(package="maps")'.  #



Attaching package: 'maps'

The following object is masked from 'package:cluster':

    votes.repub

Loading required package: ggplot2
Loading required package: gplots

Attaching package: 'gplots'

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    space

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    space

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    lowess

Loading required package: gridExtra

Attaching package: 'gridExtra'

The following object is masked from 'package:BiocGenerics':

    combine

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
Loading required package: illuminaio
Loading required package: methylumi
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")'.


Attaching package: 'Biobase'

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

    anyMissing, rowMedians

Loading required package: scales
Loading required package: reshape2
Loading required package: FDb.InfiniumMethylation.hg19
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi

Attaching package: 'AnnotationDbi'

The following object is masked from 'package:MASS':

    select

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: org.Hs.eg.db

Loading required package: minfi
Loading required package: lattice
Loading required package: SummarizedExperiment

Attaching package: 'SummarizedExperiment'

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Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    mismatch, pattern

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: plyr

Attaching package: 'plyr'

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    count

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    rename

Warning message:
replacing previous import 'gridExtra::combine' by 'methylumi::combine' when loading 'RnBeads' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RnBeads/M-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: M,RnBeadRawSet-method
> ### Title: M-methods
> ### Aliases: M M,RnBeadRawSet-method
> 
> ### ** Examples
> 
> ## No test: 
> library(RnBeads.hg19)
> data(small.example.object)
> M.intensity<-M(rnb.set.example)
> head(M.intensity)
     5815381013_R03C01 5815381013_R05C02 5815381013_R02C01 5815381013_R04C02
[1,]             16781             17096             15753             17191
[2,]             20360             20248             18280             19533
[3,]             18826             19608             16931             19244
[4,]             21972             24487             20954             22183
[5,]             20029             24664             19166             22365
[6,]             17336             19594             16296             18149
     5815381013_R01C01 5815381013_R03C02 5815381013_R02C02 5815381013_R01C02
[1,]             14139             15976             15940             16607
[2,]             18548             18511             19673             18697
[3,]             16858             16952             17130             16416
[4,]             18585             22208             20932             19344
[5,]             18288             21444             20313             18343
[6,]             15954             16455             16713             17198
     5815381013_R06C02 5815381013_R04C01 5815381013_R06C01 5815381013_R05C01
[1,]             17867             17362             18618             17638
[2,]             23222             20888             22344             21358
[3,]             20533             18409             20618             19767
[4,]             23528             23437             24740             23063
[5,]             22978             21992             24077             21586
[6,]             20237             17001             19140             18233
> ## End(No test) 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>