methLevel-MethPat-method: Compute methylation levels.

In PeteHaitch/MethylationTuples: Tools for analysing methylation patterns at genomic tuples

Description

Compute methylation levels.

Usage

## S4 method for signature 'MethPat'
methLevel(object, statistic = c("beta-values",
  "M-values"), min_cov = 1L, offset = 1L)

Arguments

object	A MethPat object containing 1-tuples.
statistic	A character string indicating which methylation level statistic is to be computed. One of "beta-values" or "M-values" (see below).
min_cov	An integer specifying the minimum coverage required in order to compute a beta-value. Samples/sites with coverage less than min_cov will have the corresponding methylation level set to NA.
offset	A numeric vector with length 1 used when computing M-values (default: 1).

Details

TODO: Define beta-values and M-values. Note any differences with how others define beta-values or M-values, e.g., minfi.

Value

A matrix, with the same dimensions and dimension names as object, of methylation levels at each methylation loci in each sample.

PeteHaitch/MethylationTuples documentation built on May 8, 2019, 1:30 a.m.