MethylToSNP: This method identifies novel SNPs in Illumina DNA methylation...

In elnitskilab/MethylToSNP: This method identifies novel SNPs in Illumina DNA methylation array data

Description

This method identifies novel SNPs in Illumina DNA methylation array data

Identify sites that may have underlying SNPs in methylation array data

Usage

MethylToSNP(
  data,
  gap.ratio = 0.75,
  gap.sum.ratio = 0.5,
  verbose = FALSE,
  outlier.sd = 3,
  SNP
)

Arguments

data	A matrix or a data frame or an GenomicRatioSet, GenomicMethylSet, MethylSet, or RatioSet object (see minfi package)
gap.ratio	The ratio of two gaps should be above the threshold.
gap.sum.ratio	The ratio of the sum of two gaps relative to the total range of values should be above the threshold.
verbose	Show additional information. Useful for debugging.
outlier.sd	Do not consider outliers that are more than the specified number of standard deviations from the cluster center.
SNP	Optional SNP annotation

Value

Detected probes with 3-tier SNP-like methylation pattern along with their reliability scores and SNP annotation

Examples

MethylToSNP(
data.frame(row.names=c('cg0000001', 'cg0000002'), sample1=c(0.1, 0.5), sample2=c(0.5, 0.9), sample3=c(0.4, 0.8)))

elnitskilab/MethylToSNP documentation built on March 21, 2020, 1:13 p.m.