Sample dataset to MethPed package.

Description

Methylation beta-values generated with the Infinium HumanMethylation450 BeadChips (Illumina).

Usage

data(MethPed_sample)

Format

A data frame with 468821 probes and 2 tumor samples

Value

DNA Methylation beta-values

References

[1] Anna Danielsson, Szil<c3><83><c2><a1>rd Nemes, Magnus Tisell, Birgitta Lannering, Claes Nordborg, Magnus Sabel, and Helena Car<c3><83><c2><a9>n. "MethPed: A DNA Methylation Classifier Tool for the Identification of Pediatric Brain Tumor Subtypes". Clinical Epigenetics 2015, 7:62, 2015

See Also

See http://www.clinicalepigeneticsjournal.com/content/7/1/62 for more details.

Examples

#################### Loading and view sample data
data(MethPed_sample)
head(MethPed_sample)

#################### Check dimention of sample data
dim(MethPed_sample)  # Check number of probes and samples in data

#################### Checking missing value in the data
missingIndex <- checkNA(MethPed_sample)

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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> library(MethPed)
Loading required package: 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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MethPed/MethPed_sample.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MethPed_sample
> ### Title: Sample dataset to MethPed package.
> ### Aliases: MethPed_sample
> ### Keywords: data
> 
> ### ** Examples
> 
> #################### Loading and view sample data
> data(MethPed_sample)
> head(MethPed_sample)
ExpressionSet (storageMode: lockedEnvironment)
assayData: 1 features, 2 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: Tumor.A Tumor.B
  varLabels: Patient_ID
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: IlluminaHumanMethylation450k 
> 
> #################### Check dimention of sample data
> dim(MethPed_sample)  # Check number of probes and samples in data
Features  Samples 
  468821        2 
> 
> #################### Checking missing value in the data
> missingIndex <- checkNA(MethPed_sample)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>