calcNormCounts

Normalizes raw counts from <code>counts</code> slot in <code>TapestriExperiment</code> and returns the object with normalized counts in the <code>normcounts</code> slot.
Also calculates the standard deviation for each probe using normalized counts and adds it to <code>rowData</code>.

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

calcNormCounts function

<dl><dt>TapestriExperiment</dt>
<dd><code>TapestriExperiment</code> object.</dd>
<dt>method</dt>
<dd>Character, normalization method. Default "mb".</dd>
<dt>scaling.factor</dt>
<dd>Numeric, optional number to scale normalized counts if <code>method == "libNorm"</code>. Default <code>NULL</code>.</dd></dl>

Arguments

Normalize raw counts — calcNormCounts

<dl>

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


<dt>method</dt>
<dd>Character, normalization method. Default "mb".</dd>


<dt>scaling.factor</dt>
<dd>Numeric, optional number to scale normalized counts if <code>method == "libNorm"</code>. Default <code>NULL</code>.</dd>

</dl>

calcNormCounts: Normalize raw counts

Description

Usage

Value

Arguments

Details

Examples