binomialTestMethylation: Call methylation status

In methimpute: Imputation-guided re-construction of complete methylomes from WGBS data

Description

Call methylation status of cytosines (or bins) with a binomial test.

Usage

binomialTestMethylation(data, conversion.rate, min.coverage = 3,
  p.threshold = 0.05)

Arguments

data	A methimputeData object.
conversion.rate	A conversion rate between 0 and 1.
min.coverage	Minimum coverage to consider for the binomial test.
p.threshold	Significance threshold between 0 and 1.

Details

The function uses a binomial test with the specified conversion.rate. P-values are then multiple testing corrected with the Benjamini & Yekutieli procedure. Methylated positions are selected with the p.threshold.

Value

A vector with methylation statuses.

Examples

## Get some toy data
file <- system.file("data","arabidopsis_toydata.RData", package="methimpute")
data <- get(load(file))
data$binomial <- binomialTestMethylation(data, conversion.rate=0.998)

methimpute documentation built on Nov. 8, 2020, 5:47 p.m.