CNV.load

Description

Prepare combined intensities from various input objects.

Usage

CNV.load(input, ...)

## S4 method for signature 'MethylSet'
CNV.load(input, names = NULL)

## S4 method for signature 'data.frame'
CNV.load(input, names = NULL)

## S4 method for signature 'matrix'
CNV.load(input, names = NULL)

## S4 method for signature 'numeric'
CNV.load(input, names = NULL)

Arguments

Details

This method gathers combined intensities of the Methylated and Unmethylated signals for all supplied probes. Probe IDs must be supplied as row names or in a seperate column named 'ID_REF' or 'TargetID'. If column names match 'intensity', only those columns are used. Else, if column names match 'signal' or 'methylated', only those columns are used. Otherwise, all columns are used.

Value

CNV.data object.

Author(s)

Volker Hovestadt conumee@hovestadt.bio

Examples

library(minfiData)
d <- CNV.load(MsetEx)
d

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(conumee)
Loading required package: minfi
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: 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: lattice
Loading required package: GenomicRanges
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: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
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: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/conumee/CNV.load.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CNV.load
> ### Title: CNV.load
> ### Aliases: CNV.load CNV.load,MethylSet-method CNV.load,data.frame-method
> ###   CNV.load,matrix-method CNV.load,numeric-method
> 
> ### ** Examples
> 
> library(minfiData)
> d <- CNV.load(MsetEx)
> d
CNV data object
   created   : 
  @intensity : available (6 samples, 485512 probes)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>