R: Plot conditional probability of samples that belongs to...
plot.methped
R Documentation
Plot conditional probability of samples that belongs to different tumor subtypes.
Description
Plot conditional probability of samples that belongs to different tumor subtypes.
Usage
## S3 method for class 'methped'
plot(x, ...)
Arguments
x
Object in "methped" class. Output of function MethPed.
...
More arguments from function barplot.
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)
#################### Plot conditional probability
plot(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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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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(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/plot.methped.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.methped
> ### Title: Plot conditional probability of samples that belongs to
> ### different tumor subtypes.
> ### Aliases: plot.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: 2.31% 7.14% 2.08% 0.00% 1.12% 8.11% 0.90% 0.00% 0.00% 6.90%
200: 2.49% 10.71% 2.08% 0.00% 1.12% 10.81% 0.90% 0.00% 0.00% 5.17%
300: 2.31% 7.14% 4.17% 0.00% 1.69% 8.11% 0.90% 0.00% 0.00% 3.45%
400: 1.78% 7.14% 2.08% 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: 1.78% 7.14% 2.08% 0.00% 1.12% 8.11% 0.90% 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: 1.78% 10.71% 2.08% 0.00% 1.12% 8.11% 0.00% 0.00% 0.00% 1.72%
900: 1.60% 7.14% 2.08% 0.00% 1.12% 8.11% 0.00% 0.00% 0.00% 1.72%
1000: 1.78% 10.71% 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
>
> #################### Plot conditional probability
> plot(res)
Error in dev.new() : no suitable unused file name for pdf()
Calls: plot -> plot.methped -> par -> resetPar -> dev.new
Execution halted
providing 
.