background_error_rate

background_error_rate.txt

This table contains 9 variables for each genomic position<ul>
<li><code>chrpos</code>, char, of the form chrN:XXXXXXXXX defining genomic position</li>
<li><code>N0</code>, integer, the coverture in the controls</li>
<li><code>E0</code>, integer, the number of errors in the controls</li>
<li><code>p.sain</code>, numeric, the ratio E0/N0</li>
<li><code>up.sain</code>, numeric, the 95th quantile of the Binomial with parameter N0 and E0/N0</li>
<li><code>E0indel</code>, integer, the amount of indel</li>
<li><code>indel.p.sain</code>, numeric, the ration E0indel/N0</li>
<li><code>indel.up.sain</code>, numeric, the 95th quantile of the Binomial with parameter N0 and E0indel/N0</li>
<li><code>hotspot</code>, char, either 'Non-hotspot' or 'Hotspot' depending if the genomic position is known as hotspot or not.</li>
</ul>

data

Aims at detecting single nucleotide variation
(SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used
as a surrogate marker for tumor, at each base position of an Next Generation
Sequencing (NGS) analysis. Mutations are assessed by comparing the minor-allele
frequency at each position to the measured PER in control samples.

Yves Rozenholc

PlasmaMutationDetector

Tumor Mutation Detection in Plasma

background_error_rate function

The package provide the SNV and INDEL PERs computed for the Ion AmpliSeq&lt;U+2122&gt; Colon and Lung Cancer Panel v2 from 29 controls in a table available in the data file <code>background_error_rate.txt</code>. — background_error_rate

The package provide the SNV and INDEL PERs computed for the Ion AmpliSeq&lt;U+2122&gt; Colon and Lung Cancer Panel v2 from 29 controls in a table available in the data file <code>background_error_rate.txt</code>.

background_error_rate: The package provide the SNV and INDEL PERs computed for the Ion AmpliSeq<U+2122> Colon and Lung Cancer Panel v2 from 29 controls in a table available in the data file `background_error_rate.txt`.

Description

Usage

Arguments

References

See Also