README.md

In fynnwi/intratumormeth: Intratumor DNA Methylation Analysis

intratumormeth

The goal of this package is to facilitate analysis of DNA methylation data obtained from Illumina MethylationEPIC platform for multiple samples of the same tumor.

Installation

You can install the development version of intratumormeth from GitHub with:

# install.packages("devtools")
devtools::install_github("fynnwi/intratumormeth")

Workflow

Every stage of the analysis pipeline is described in a separate vignette (see articles):

1. preprocessing: read IDAT files, extract methylation values
2. quality_control: investigate detection p-values, tumor purity, find poor quality samples and probes
3. copynumber: run conumee and generate CNV data
4. classification: evaluate glioma subtype and MGMT promoter methylation
5. dimensionality_reduction: perform PCA and t-SNE to find clusters
6. phylogeny: run TuMult to find phylogeny from CNV data

fynnwi/intratumormeth documentation built on March 29, 2022, 12:06 a.m.