MethylDiff

Using a chromDictMeth() output object, quickly calculate the mean methylation difference across a user-specified region.

A system for fast, accurate, and flexible whole genome bisulfite sequencing (WGBS) data analysis of two-condition comparisons. Principal Component BiSulfite, 'PCBS', assigns methylated loci eigenvector values from the treatment-delineating principal component in lieu of running millions of pairwise statistical tests, which dramatically increases analysis flexibility and reduces computational requirements. Methods: <https://katlande.github.io/PCBS/articles/Differential_Methylation.html>.

Kathryn Lande

PCBS

Principal Component BiSulfite

MethylDiff function

<dl><dt>chromDictMeth</dt>
<dd>chromDictMeth() output object</dd><dt>chrom</dt>
<dd><code>character</code>, chromosome</dd><dt>start</dt>
<dd><code>integer</code>, region start</dd><dt>end</dt>
<dd><code>integer</code>, region end</dd></dl>

Arguments

Get the mean methylation difference across a specified region. — MethylDiff

<dl>

<dt>chromDictMeth</dt>
<dd>chromDictMeth() output object</dd>

<dt>chrom</dt>
<dd><code>character</code>, chromosome</dd>

<dt>start</dt>
<dd><code>integer</code>, region start</dd>

<dt>end</dt>
<dd><code>integer</code>, region end</dd>

</dl>

MethylDiff: Get the mean methylation difference across a specified region.

Description

Usage

Value

Arguments

Examples