vcflocus

Creates a string with the information for all SNPs. The information is coded
as R,A:DP. R is the number of reads of the reference allele, A is the number
of reads of the alternative allele and DP is the total depth of coverage.
Each entry of the character string corresponds to a different SNP.

internal

Simulates pooled sequencing data under a variety of conditions.
Also allows for the evaluation of the average absolute difference between allele frequencies
computed from genotypes and those computed from pooled data.
Carvalho et al., (2022) <doi:10.1101/2023.01.20.524733>.

João Carvalho

poolHelper

Simulates Pooled Sequencing Genetic Data

Vítor Sousa

vcflocus function

<dl><dt>reference</dt>
<dd>is a vector with the number of reads with the reference
allele. Each entry of the vector corresponds to a different SNP.</dd>
<dt>alternative</dt>
<dd>is a vector with the number of reads with the alternative
allele. Each entry of the vector corresponds to a different SNP.</dd>
<dt>total</dt>
<dd>is a vector with the total number of reads observed at each SNP.
Each entry of the vector corresponds to a different SNP.</dd></dl>

Arguments

Create vcf string for all SNPs in a single locus — vcflocus

<dl>

<dt>reference</dt>
<dd>is a vector with the number of reads with the reference
allele. Each entry of the vector corresponds to a different SNP.</dd>


<dt>alternative</dt>
<dd>is a vector with the number of reads with the alternative
allele. Each entry of the vector corresponds to a different SNP.</dd>


<dt>total</dt>
<dd>is a vector with the total number of reads observed at each SNP.
Each entry of the vector corresponds to a different SNP.</dd>

</dl>

vcflocus: Create vcf string for all SNPs in a single locus

Description

Usage

Value

Arguments