cometh: Estimate within-sample, within-fragment co-methylation using...

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

Description

Estimate within-sample, within-fragment co-methylation using 2-tuples.

Usage

cometh(methpat, pair_type = c("all", "strict_adjacent"), ref_loci,
  method = c("lor", "pearson"), min_cov = 5L, alternative = c("two.sided",
  "less", "greater"), conf.level = 0.95, feature, offset = 0.5)

Arguments

methpat	A MethPat object containing 2-tuples.
pair_type	A character string giving the type of pairs to be constructed when computing correlations. One of "neighbours" or "all", can be abbreviated. Please see the below section, "Choice of 'pair_type'", for details.
method	A character string indicating which statistic to use to estimate co-methylation. This must be (an abbreviation of) one of the strings "lor" (log_{2}(odds-ratio)) or "pearson" (Pearson product-moment correlation coefficient). Please see the below section, "Choice of statistic", for details.
min_cov	An integer specifying the minimum coverage required in order to use a 2-tuple when estimating co-methylation.
alternative	Indicates the alternative hypothesis and must be one of "two.sided", "greater" or "less". You can specify just the initial letter. "greater" corresponds to positive association, "less" to negative association.
feature	An optional GRanges object with the locations of a "genomic feature". This GRanges object must be disjoint (see isDisjoint). Please see the below section, "Stratifying pairs by a genomic feature", for details.
offset	A numeric vector with length 1 used when computing M-values (default: 0.5).

Choice of 'pair_type'

TODO

Choice of statistic

TODO

Stratifying pairs by a genomic feature

TODO

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