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---
title: "Classifiers methods"
bibliography: bibliography.bib
vignette: >
%\VignetteIndexEntry{10. Classifiers}
%\VignetteEngine{knitr::rmarkdown}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(dpi = 300)
knitr::opts_chunk$set(cache = FALSE)
```
```{r, echo = FALSE,hide=TRUE, message=FALSE,warning=FALSE}
library(TCGAbiolinks)
```
```{r message=FALSE, warning=FALSE, include=FALSE}
library(SummarizedExperiment)
library(dplyr)
library(DT)
```
<br>
## Classifying gliomas samples with `gliomaClassifier`
<hr>
Classifying glioma samples with DNA methylation array based on:
**Ceccarelli, Michele, et al. "Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma." Cell 164.3 (2016): 550-563.** (https://doi.org/10.1016/j.cell.2015.12.028)
Possible classifications are:
- Mesenchymal-like
- Classic-like
- G-CIMP-high
- G-CIMP-low
- LGm6-GBM
- Codel
## Data
<hr>
The input data can be either a Summarized Experiment object of a matrix
(samples as columns, probes as rows) from the following platforms:
- HM27
- HM450
- EPIC array.
In this example we will retrieve two samples from TCGA and classify them expecting
the same result as the paper.
```{r, eval = FALSE, message = FALSE, results = "hide"}
query <- GDCquery(
project = "TCGA-GBM",
data.category = "DNA methylation",
barcode = c("TCGA-06-0122","TCGA-14-1456"),
platform = "Illumina Human Methylation 27",
legacy = TRUE
)
GDCdownload(query)
data.hg19 <- GDCprepare(query)
```
```{r, eval = FALSE}
assay(data.hg19)[1:5,1:2]
```
## Function
<hr>
```{r, eval = FALSE}
classification <- gliomaClassifier(data.hg19)
```
## Results
<hr>
The classfier will return a list of 3 data frames:
1. Sample final classification
2. Each model final classification
3. Each class probability of classification
```{r, eval = FALSE}
names(classification)
classification$final.classification
classification$model.classifications
classification$model.probabilities
```
## Comparing results with paper
<hr>
```{R}
TCGAquery_subtype("GBM") %>%
dplyr::filter(patient %in% c("TCGA-06-0122","TCGA-14-1456")) %>%
dplyr::select("patient","Supervised.DNA.Methylation.Cluster")
```
|
