DefineBestPC

Defines the best principle component to use for downstream analysis.

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

DefineBestPC function

<dl><dt>mat</dt>
<dd>Bismark2Matrix.R output file, or data frame object</dd><dt>IDs</dt>
<dd>A character vector of IDs containing the common names for compared conditions. E.g., for samples trt1, trt2 vs. ctl1, ctl2, IDs=c("trt", "ctl")</dd><dt>filter_thresh</dt>
<dd>A coverage threshold for filtering, where CpG coverage of all samples must be larger than this value</dd><dt>return.plot</dt>
<dd>T/F, whether to return a PCA plot or a numeric representing the best principle component for downstream analysis</dd></dl>

Arguments

Identify your best principle component. — DefineBestPC

<dl>

<dt>mat</dt>
<dd>Bismark2Matrix.R output file, or data frame object</dd>

<dt>IDs</dt>
<dd>A character vector of IDs containing the common names for compared conditions. E.g., for samples trt1, trt2 vs. ctl1, ctl2, IDs=c("trt", "ctl")</dd>

<dt>filter_thresh</dt>
<dd>A coverage threshold for filtering, where CpG coverage of all samples must be larger than this value</dd>

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

</dl>

DefineBestPC: Identify your best principle component.

Description

Usage

Value

Arguments

Examples