Summary of conditional probability or binary classification of samples that belong to different tumor subtypes.

Description

Summary of conditional probability or binary classification of samples that belong to different tumor subtypes.

Usage

## S3 method for class 'methped'
summary(object, ...)

Arguments

Value

Object in "methped" class. Output of function MethPed.

Examples

#################### Loading sample data
data(MethPed_sample)

#################### Applying MethPed to sample data
res<-MethPed(MethPed_sample)

#################### Summary function of MethPed output
summary (res)

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
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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/summary.methped.Rd_%03d_medium.png", width=480, height=480)
> ### Name: summary.methped
> ### Title: Summary of conditional probability or binary classification of
> ###   samples that belong to different tumor subtypes.
> ### Aliases: summary.methped
> 
> ### ** Examples
> 
> 
> #################### Loading sample data
> data(MethPed_sample)
> 
> #################### Applying MethPed to sample data
> res<-MethPed(MethPed_sample)

Probe's column name in data                 : TargetID
Probe name integrity of data with predictor : OK
Missing value in data                       : No missing data point
Data summary                                : 468821 Probes and 2 Sample 


Initiating  data analysis......

Classification is being processed on 1000 tree

ntree      OOB      1      2      3      4      5      6      7      8      9
  100:   1.78%  7.14%  2.08%  0.00%  1.12%  8.11%  0.90%  0.00%  0.00%  1.72%
  200:   2.31% 10.71%  4.17%  0.00%  1.12%  8.11%  1.80%  0.00%  0.00%  1.72%
  300:   2.13% 10.71%  4.17%  0.00%  1.69%  8.11%  0.00%  0.00%  0.00%  1.72%
  400:   1.95%  7.14%  4.17%  0.00%  1.12%  8.11%  0.90%  0.00%  0.00%  1.72%
  500:   1.60%  7.14%  2.08%  0.00%  1.12%  8.11%  0.00%  0.00%  0.00%  1.72%
  600:   1.60%  7.14%  2.08%  0.00%  1.12%  8.11%  0.00%  0.00%  0.00%  1.72%
  700:   1.60%  7.14%  2.08%  0.00%  1.12%  8.11%  0.00%  0.00%  0.00%  1.72%
  800:   1.60%  7.14%  2.08%  0.00%  1.12%  8.11%  0.00%  0.00%  0.00%  1.72%
  900:   1.78%  7.14%  2.08%  0.00%  1.69%  8.11%  0.00%  0.00%  0.00%  1.72%
 1000:   1.60%  7.14%  2.08%  0.00%  1.12%  8.11%  0.00%  0.00%  0.00%  1.72%

Missing probes: 1 out of 900 probes are missing

Finished analysis data


> 
> #################### Summary function of MethPed output
> summary (res)
         DIPG Ependymoma  ETMR   GBM MB_Gr3 MB_Gr4 MB_SHH MB_WNT PiloAstro
Tumor.A 0.004      0.074 0.008 0.031  0.798  0.046  0.009  0.021     0.009
Tumor.B 0.003      0.041 0.003 0.194  0.001  0.001  0.001  0.000     0.756
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>