error_table

A precomputed table reporting for different combinations of coverage and
number of informative SNPs the expected error of the beta value computed by
function <code><a rd-options="CLONETv2:compute_beta_table" href="/link/compute_beta_table?package=CLONETv2&version=2.2.1&to=CLONETv2%3Acompute_beta_table" data-mini-rdoc="CLONETv2:compute_beta_table::compute_beta_table">compute_beta_table</a></code>.

datasets

Analyze data from next-generation sequencing experiments on genomic samples. 'CLONETv2' offers a set of functions to compute allele specific copy number and clonality from segmented data and SNPs position pileup. The package has also calculated the clonality of single nucleotide variants given read counts at mutated positions. The package has been developed at the laboratory of Computational and Functional Oncology, Department of CIBIO, University of Trento (Italy), under the supervision of prof Francesca Demichelis. References: Prandi et al. (2014) <doi:10.1186/s13059-014-0439-6>; Carreira et al. (2014) <doi:10.1126/scitranslmed.3009448>; Romanel et al. (2015) <doi:10.1126/scitranslmed.aac9511>.

Yari Ciani

CLONETv2

Clonality Estimates in Tumor

Davide Prandi

Alessandro Romanel

Tarcisio Fedrizzi

error_table function

A data frame column names mean.cov, n.info.snps, and
adm.estimation.error<dl class="dl-horizontal">
<dt>mean.cov</dt><dd>genomic segment coverage</dd>
<dt>n.info.snps</dt><dd>number of informative SNPs</dd>
<dt>adm.estimation.error</dt><dd>expected error on beta estimate</dd> </dl>

Format

A precomputed table reporting for different combinations of coverage and
number of informative SNPs the expected error of the beta value computed by
function <code><a rd-options='CLONETv2:compute_beta_table' href='compute_beta_table'>compute_beta_table</a></code>.

Beta estimation error. — error_table

A data frame column names mean.cov, n.info.snps, and
adm.estimation.error<dl class='dl-horizontal'>
<dt>mean.cov</dt><dd>genomic segment coverage</dd>
<dt>n.info.snps</dt><dd>number of informative SNPs</dd>
<dt>adm.estimation.error</dt><dd>expected error on beta estimate</dd> </dl>

error_table: Beta estimation error.

Description

Usage

Arguments

Format