binomialTestMethylation: Call methylation status

Description Usage Arguments Details Value Examples

View source: R/callMethylation.R

Description

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

Usage

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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

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## 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.