binomialTestMethylation {methimpute} | R Documentation

## Call methylation status

### 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)

[Package methimpute version 1.6.0 Index]