RCNA_object-class

RCNA_object

An S4 class used to specify parameters for an analysis run

Detects copy number alteration events in targeted exon sequencing
data for tumor samples without matched normal controls. The advantage of
this method is that it can be applied to smaller sequencing panels including
evaluations of exon, transcript, gene, or even user specified genetic
regions of interest. Functions in the package include steps for GC-content
correction, calculation of quantile based normal karyotype ranges,
and calculation of feature score.  Cutoffs for "normal" quantile and score
are user-adjustable.

Matt Bradley

RCNA

Robust Copy Number Alteration Detection (RCNA)

RCNA_object-class function

<dl>
<dt><code>sample.names</code></dt>
<dd>Required. Character vector containing names of subjects</dd></dl>
<dt><code>ano.file</code></dt>
<dd>Required. Character single file path detailing a feature-wise annotation file</dd>
<dt><code>out.dir</code></dt>
<dd>Required. Character vector containing the name of each subject?s output directory</dd>
<dt><code>gcParams</code></dt>
<dd>Data Frame storing all run parameters for the correct_gc_bias function</dd>
<dt><code>nkrParams</code></dt>
<dd>Data Frame storing all run parameters for the estimate_nkr function</dd>
<dt><code>scoreParams</code></dt>
<dd>Data Frame storing all run parameters for the estimate_feature_score function</dd>
<dt><code>commands</code></dt>
<dd>RCNA_analysis object storing commands and parameters from previous function runs on this object</dd>

Slots

RCNA.object definition — RCNA_object-class

<dl>
<dt><code>sample.names</code></dt>
<dd>Required. Character vector containing names of subjects</dd>


<dt><code>ano.file</code></dt>
<dd>Required. Character single file path detailing a feature-wise annotation file</dd>


<dt><code>out.dir</code></dt>
<dd>Required. Character vector containing the name of each subject?s output directory</dd>


<dt><code>gcParams</code></dt>
<dd>Data Frame storing all run parameters for the correct_gc_bias function</dd>


<dt><code>nkrParams</code></dt>
<dd>Data Frame storing all run parameters for the estimate_nkr function</dd>


<dt><code>scoreParams</code></dt>
<dd>Data Frame storing all run parameters for the estimate_feature_score function</dd>


<dt><code>commands</code></dt>
<dd>RCNA_analysis object storing commands and parameters from previous function runs on this object</dd>


</dl>

RCNA_object-class: RCNA.object definition

Description

Arguments

Slots

See Also