MethylToSNP: identifying SNPs in Illumina DNA methylation array data.

ABSTRACT:

Background

Current array-based methods for the measurement of DNA methylation rely on the process of sodium bisulfite conversion to differentiate between methylated and unmethylated cytosine bases in DNA. In the absence of genotype data this process can lead to ambiguity in data interpretation when a sample has polymorphisms at a methylation probe site. A common way to minimize this problem is to exclude such potentially problematic sites, with some methods removing as much as 60% of array probes from consideration before data analysis.

Results

Here, we present an algorithm implemented in an R Bioconductor package, MethylToSNP, which detects a characteristic data pattern to infer sites likely to be confounded by polymorphisms. Additionally, the tool provides a stringent reli

SUBMITTER: LaBarre BA 

PROVIDER: S-EPMC6923858 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature