Get_Novel_DMRs

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

Get_Novel_DMRs function

<dl><dt>ranks</dt>
<dd>Rank data frame from getPCRanks.</dd><dt>nSeeds</dt>
<dd>Integer, number of input seeds for DMR expansion.</dd><dt>chromDictObj</dt>
<dd>chromDict() output. If null, chromDict() is run internally.</dd><dt>DMR_resolution</dt>
<dd>Automatic=NULL. Integer, number of bases to increase the DMR by with each expansion. If NULL, QueryLimit/25.</dd><dt>QueryLimit</dt>
<dd>Automatic=5000. Maximum DMR expansion size (bp)</dd><dt>minCpGs</dt>
<dd>Automatic=15. Minimum CpGs in a DMR region, regions with fewer CpGs will be discarded.</dd><dt>minZ</dt>
<dd>Automatic=1. Absolute Z score threshold for DMR calling; internal value. Not recommended to play with this setting.</dd><dt>perms</dt>
<dd>Automatic=1000. Number of permutations to use when defining the null distribution. Increasing this value largely influences computational time with minimal return</dd></dl>

Arguments

Call DMRs from WGBS data. — Get_Novel_DMRs

<dl>

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

<dt>nSeeds</dt>
<dd>Integer, number of input seeds for DMR expansion.</dd>

<dt>chromDictObj</dt>
<dd>chromDict() output. If null, chromDict() is run internally.</dd>

<dt>DMR_resolution</dt>
<dd>Automatic=NULL. Integer, number of bases to increase the DMR by with each expansion. If NULL, QueryLimit/25.</dd>

<dt>QueryLimit</dt>
<dd>Automatic=5000. Maximum DMR expansion size (bp)</dd>

<dt>minCpGs</dt>
<dd>Automatic=15. Minimum CpGs in a DMR region, regions with fewer CpGs will be discarded.</dd>

<dt>minZ</dt>
<dd>Automatic=1. Absolute Z score threshold for DMR calling; internal value. Not recommended to play with this setting.</dd>

<dt>perms</dt>
<dd>Automatic=1000. Number of permutations to use when defining the null distribution. Increasing this value largely influences computational time with minimal return</dd>

</dl>

Get_Novel_DMRs: Call DMRs from WGBS data.

Description

Usage

Value

Arguments

Examples