beta2genotype: converts beta-values to genotypes (1, 2 and 3)

In omicsPrint: Cross omic genetic fingerprinting

Description

convert DNA methylation beta-value to inferred genotypes

Usage

beta2genotype(betas, na.rm = TRUE, minSep = 0.25, minSize = 5,
  centers = c(0.2, 0.5, 0.8), assayName = NULL)

Arguments

betas	beta matrix of probes possibly affected SNPs; if this is a SummarizedExperiment or a MultiAssayExperiment assayName must also be specified
na.rm	TRUE drop cpg for which no clustering was observed
minSep	minimal separation between clusters
minSize	size of smallest cluster (in percentage)
centers	center of clusters, defaults to 0.2, 0.5, 0.8.
assayName	the name of the assay to be used (see betas)

Details

Using kmeans unsupervised clustering to infer genotypes based on idea's from Leonard Schalkwyk; wateRmelon packages.

'minSep' and 'minSize' ensure good clusters are found. This function is similar to the gaphunter approach implemented in minfi.

Value

matrix with genotypes

Author(s)

mvaniterson

Examples

set.seed(12345)
beta <- matrix(runif(100*10, 0,1), nrow=100)
beta[1:5, 1:5]
genotype <- beta2genotype(beta)
genotype[1:5, 1:5]

omicsPrint documentation built on Nov. 8, 2020, 4:55 p.m.