List of 900 probes in the predictor (Training data for Random Forest model)
Usage
data(MethPed_900probes)
Format
Data frame of 900 probes.
Details
For the construction of the training probe pool (predictors), methylation data generated by
the Illumina Infinium HumanMethylation 450 BeadChip arrays were downloaded from the Gene Expression
Omnibus (GEO). Four hundred seventy-two cases were available, representing several brain tumor diagnoses
(DIPG, glioblastoma, ETMR, medulloblastoma, ependymoma, pilocytic astrocytoma) and their further subgroups.
The data sets were merged and probes that did not appear in all data sets were filtered away. In addition,
about 190,000 CpGs were removed due to SNPs, repeats and multiple mapping sites. The final data set contained
206,823 unique probes and nine tumor classes including the medulloblastoma subgroups. K<c3><a2><c2><80><c2><93>neighbor imputation
was used for missing probe data.
After that, a large number of regression analyses were performed to select the 100 probes per tumor class that
had the highest predictive power (AUC values). Based on the identified 900 methylation sites, the nine pediatric
brain tumor types could be accurately classified using the multiclass classification algorithm MethPed.
Value
450k methylation array probe name
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
#################### Loading and view sample data
data(MethPed_900probes)
head(MethPed_900probes)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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_900probes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MethPed_900probes
> ### Title: List of 900 probes in the predictor data
> ### Aliases: MethPed_900probes
> ### Keywords: data
>
> ### ** Examples
>
> #################### Loading and view sample data
> data(MethPed_900probes)
> head(MethPed_900probes)
TargetID
1 cg00001930
2 cg00013409
3 cg00015639
4 cg00036119
5 cg00061695
6 cg00085790
>
>
>
>
>
>
> dev.off()
null device
1
>