Input_Example

A dataset generated by:
Input_Example&lt;-QuantumCat(number_of_clones = 4,
 number_of_mutations = 100,
 ploidy = "AB",depth = 150,
 number_of_samples = 2,
 contamination = c(0,0))

datasets

Using HTS data, clusters mutations in order to recreate putative
clones from the data provided. It requires genotype at the location of the
variant as well as the depth of coverage and number of reads supporting the
mutation. Additional information may be provided, such as the contamination
in the tumor sample. This package also provides a function QuantumCat() which
simulates data obtained from tumor sequencing.

Paul Deveau

QuantumClone

Clustering Mutations using High Throughput Sequencing (HTS) Data

Input_Example function

A list of dataframes<dl class="dl-horizontal">
 <dt>SampleName</dt><dd>First column containing the name of the sample</dd>
 <dt>Chr</dt><dd>The chromosome either 1 2 ... X Y or chr1 chr2 ... chrY</dd>
 <dt>Start</dt><dd>The genomic position of the variant</dd>
 <dt>Alt</dt><dd>Number of reads supporting variant allele</dd>
 <dt>Depth</dt><dd>Total number of reads (reference + alternative allele) at position</dd>
</dl>

Format

Example generated by QuantumCat — Input_Example

A list of dataframes<dl class='dl-horizontal'>
 <dt>SampleName</dt><dd>First column containing the name of the sample</dd>
 <dt>Chr</dt><dd>The chromosome either 1 2 ... X Y or chr1 chr2 ... chrY</dd>
 <dt>Start</dt><dd>The genomic position of the variant</dd>
 <dt>Alt</dt><dd>Number of reads supporting variant allele</dd>
 <dt>Depth</dt><dd>Total number of reads (reference + alternative allele) at position</dd>
</dl>

Input_Example: Example generated by QuantumCat

Description

Usage

Arguments

Format