RCNA_analysis-class

RCNA_analysis

An S4 class used to track parameters from a specific RCNA function execution.

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_analysis-class function

<dl>
<dt><code>call</code></dt>
<dd>A character vector detailing the function call that (`correct_gc_bias`, `estimate_nkr`, `estimate_feature_score`) was performed to produce this S4 object.</dd></dl>
<dt><code>params</code></dt>
<dd>A list corresponding to the parameters that were submitted with the associated function call</dd>
<dt><code>res.files</code></dt>
<dd>A list containing the names of the flat files that were created by the documented function call.</dd>

Slots

RCNA_analysis constructor — RCNA_analysis-class

<dl>
<dt><code>call</code></dt>
<dd>A character vector detailing the function call that (`correct_gc_bias`, `estimate_nkr`, `estimate_feature_score`) was performed to produce this S4 object.</dd>


<dt><code>params</code></dt>
<dd>A list corresponding to the parameters that were submitted with the associated function call</dd>


<dt><code>res.files</code></dt>
<dd>A list containing the names of the flat files that were created by the documented function call.</dd>


</dl>

RCNA_analysis-class: RCNA_analysis constructor

Description

Arguments

Slots