getCytobands

<code>getCytobands()</code> retrieves the chromosome arm and cytoband for each probe based on stored positional data and saves them in <code>rowData</code>.
This is run automatically as part of <code>createTapestriExperiment()</code>.
Note: Some downstream smoothing and plotting functions may fail if chromosome arms are not present in <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

getCytobands function

<dl><dt>TapestriExperiment</dt>
<dd><code>TapestriExperiment</code> object.</dd>
<dt>genome</dt>
<dd>Character, reference genome to use. Only hg19 is currently supported.</dd>
<dt>verbose</dt>
<dd>Logical, if <code>TRUE</code> (default), progress is output as message text.</dd></dl>

Arguments

Add chromosome cytobands and chromosome arms to TapestriExperiment — getCytobands

<dl>

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


<dt>genome</dt>
<dd>Character, reference genome to use. Only hg19 is currently supported.</dd>


<dt>verbose</dt>
<dd>Logical, if <code>TRUE</code> (default), progress is output as message text.</dd>

</dl>

getCytobands: Add chromosome cytobands and chromosome arms to `TapestriExperiment`

Description

Usage

Value

Arguments

Examples