rankDist

Automated rank cut-off estimator for input CpGs.

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

rankDist function

<dl><dt>ranks</dt>
<dd>getPCRanks output data frame.</dd><dt>draw_intersects</dt>
<dd>T/F whether to draw intersect lines if return.plot=T</dd><dt>noise_perc</dt>
<dd>Automatic=0.5, numeric between 0 and 1. Fraction of ranks to use to model the background noise. Not recommended to play with this value. Increasing/decreasing returns a looser/stricter threshold, respectively.</dd><dt>mode</dt>
<dd>"intersect" or "strict", determine cut-off with "intersect" or "strict" method. "Strict" is recommended for sets with lower variability</dd><dt>return.plot</dt>
<dd>T/F, whether to return a plot or a numeric</dd></dl>

Arguments

Identify the best rank cut-off for significant CpGs. — rankDist

<dl>

<dt>ranks</dt>
<dd>getPCRanks output data frame.</dd>

<dt>draw_intersects</dt>
<dd>T/F whether to draw intersect lines if return.plot=T</dd>

<dt>noise_perc</dt>
<dd>Automatic=0.5, numeric between 0 and 1. Fraction of ranks to use to model the background noise. Not recommended to play with this value. Increasing/decreasing returns a looser/stricter threshold, respectively.</dd>

<dt>mode</dt>
<dd>"intersect" or "strict", determine cut-off with "intersect" or "strict" method. "Strict" is recommended for sets with lower variability</dd>

<dt>return.plot</dt>
<dd>T/F, whether to return a plot or a numeric</dd>

</dl>

rankDist: Identify the best rank cut-off for significant CpGs.

Description

Usage

Value

Arguments

Examples