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