getPCRanks

Returns eigenvector scores for input CpG sites.

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

getPCRanks 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 &amp; trt2 vs. ctl1 &amp; ctl2, IDs=c("trt1", "ctl")</dd><dt>PC</dt>
<dd>Integer, which principle component to use. Use to DefineBestPC if unsure.</dd><dt>filter_thresh</dt>
<dd>Integer, a coverage threshold for filtering, where CpG coverage of all samples must be larger than this value.</dd></dl>

Arguments

Get CpG eigenvector scores from a principle component. — getPCRanks

<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 &amp; trt2 vs. ctl1 &amp; ctl2, IDs=c("trt1", "ctl")</dd>

<dt>PC</dt>
<dd>Integer, which principle component to use. Use to DefineBestPC if unsure.</dd>

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

</dl>

getPCRanks: Get CpG eigenvector scores from a principle component.

Description

Usage

Value

Arguments

Examples