Skip to content

Estimate tumor enrichment from methylation array data.

Notifications You must be signed in to change notification settings

metamaden/InfiniumPurifyR

Repository files navigation

InfiniumPurifyr

Estimate tumor enrichment from methylation array data. This package is downloadable using the following in R:
require(devtools); install_github("metamaden/InfiniumPurifyr")

Description

InfiniumPurifyr (IPR) estimates tumor purity as the maximum mode in a distribution of Beta-values at differentially and variably methylated CpG probes (DMVPs, tumor vs. normal-matched samples), where hypomethylated DMVPs (tumor < normal-matched) are transformed to be 1 - Beta-value.

This package is an adaptation of the python-encoded InfiniumPurify method, described for HM450 data in Zhang et al 2016.

The workflow described in Zhang et al is as follows: alt text

The implementation in InfiniumPurifyR is as follows: alt text

Example

An example is with a set of esophageal adenocarcinoma samples with subtypes HM, IM, LM, and MM. Using DMVPs derived from TCGA EACs as in the workflow above, we generate the following unimodal distributions with plotunimod=TRUE: alt text

News

12/1/2017: An official port is offered by the original authors on CRAN here. Findings have been validated for ESCA iDMPs using both packages, and purity results are identical.

Releases

No releases published

Packages

No packages published

Languages