CheckOvercompression

Identifies if seed number to use for DMR calling causes overcompression.

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

CheckOvercompression function

<dl><dt>ranks</dt>
<dd>Rank data frame from getPCRanks.</dd><dt>CpG_cutoff</dt>
<dd>NULL or numeric. If NULL, seed numbers tested will be input of the values argument. If numeric, seed numbers tested will be CpG_cutoff*values argument. Recommended to us rankDist estimate if not null</dd><dt>values</dt>
<dd>Numeric vector, either seed numbers to test if CpG_cutoff=NULL or multipliers if CpG_cutoff is numeric</dd><dt>max.dmr.size</dt>
<dd>Automatic=5000. Maximum DMR expansion size in downstream analysis. Note: pipeline is optimized for 5000bp max DMR size, it is not recommended to play with this value.</dd><dt>return.plot</dt>
<dd>T/F, whether to return a plot or a numeric representing the best seed number for downstream analysis</dd></dl>

Arguments

Check if DMR calling seed number is ovcompressed. — CheckOvercompression

<dl>

<dt>ranks</dt>
<dd>Rank data frame from getPCRanks.</dd>

<dt>CpG_cutoff</dt>
<dd>NULL or numeric. If NULL, seed numbers tested will be input of the values argument. If numeric, seed numbers tested will be CpG_cutoff*values argument. Recommended to us rankDist estimate if not null</dd>

<dt>values</dt>
<dd>Numeric vector, either seed numbers to test if CpG_cutoff=NULL or multipliers if CpG_cutoff is numeric</dd>

<dt>max.dmr.size</dt>
<dd>Automatic=5000. Maximum DMR expansion size in downstream analysis. Note: pipeline is optimized for 5000bp max DMR size, it is not recommended to play with this value.</dd>

<dt>return.plot</dt>
<dd>T/F, whether to return a plot or a numeric representing the best seed number for downstream analysis</dd>

</dl>

CheckOvercompression: Check if DMR calling seed number is ovcompressed.

Description

Usage

Value

Arguments

Examples