PCAKneePlot

Draws "knee plot" of PCA proportion of variance explained to determine which principal components (PCs) to include for downstream applications e.g. clustering.
Variance explained for each PC is indicated by the line.
Cumulative variance explained is indicated by the bars.

Analysis of DNA copy number in single cells using
custom genome-wide targeted DNA sequencing panels for the Mission Bio
Tapestri platform. Users can easily parse, manipulate, and visualize
datasets produced from the automated 'Tapestri Pipeline', with support for
normalization, clustering, and copy number calling. Functions are also
available to deconvolute multiplexed samples by genotype and parsing
barcoded reads from exogenous lentiviral constructs.

Joseph Mays

karyotapR

DNA Copy Number Analysis for Genome-Wide Tapestri Panels

PCAKneePlot function

<dl><dt>TapestriExperiment</dt>
<dd><code>TapestriExperiment</code> object</dd>
<dt>alt.exp</dt>
<dd>Character, <code>altExp</code> to use, <code>NULL</code> uses top-level/main experiment. Default "alleleFrequency".</dd>
<dt>n.pcs</dt>
<dd>Numeric, number of PCs to plot, starting at 1. Default 10.</dd></dl>

Arguments

Plot of PCA proportion of variance explained — PCAKneePlot

<dl>

<dt>TapestriExperiment</dt>
<dd><code>TapestriExperiment</code> object</dd>


<dt>alt.exp</dt>
<dd>Character, <code>altExp</code> to use, <code>NULL</code> uses top-level/main experiment. Default "alleleFrequency".</dd>


<dt>n.pcs</dt>
<dd>Numeric, number of PCs to plot, starting at 1. Default 10.</dd>

</dl>

PCAKneePlot: Plot of PCA proportion of variance explained

Description

Usage

Value

Arguments

Examples