poolProbs

This function computes the probability of contribution of each pool towards
the total depth of coverage of a single population. If multiple pools where
used to sequence a single population, it is possible that some pools
contribute more than others.

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

poolProbs function

<dl><dt>nPools</dt>
<dd>an integer indicating how many pools were used to sequence the
population.</dd>
<dt>vector_np</dt>
<dd>is a vector where each entry contains the number of diploid
individuals of a given pool. Thus, if a population was sequenced using two
pools, each with 10 individuals, this vector would contain two entries and
both will be 10.</dd>
<dt>nSNPs</dt>
<dd>an integer indicating how many SNPs exist in the data.</dd>
<dt>pError</dt>
<dd>an integer representing the value of the error associated with
DNA pooling. This value is related with the unequal pool contribution
towards the total number of reads of a population - the higher the value
the more unequal are the pool contributions.</dd></dl>

Arguments

Probability of contribution of each pool — poolProbs

<dl>

<dt>nPools</dt>
<dd>an integer indicating how many pools were used to sequence the
population.</dd>


<dt>vector_np</dt>
<dd>is a vector where each entry contains the number of diploid
individuals of a given pool. Thus, if a population was sequenced using two
pools, each with 10 individuals, this vector would contain two entries and
both will be 10.</dd>


<dt>nSNPs</dt>
<dd>an integer indicating how many SNPs exist in the data.</dd>


<dt>pError</dt>
<dd>an integer representing the value of the error associated with
DNA pooling. This value is related with the unequal pool contribution
towards the total number of reads of a population - the higher the value
the more unequal are the pool contributions.</dd>

</dl>

poolProbs: Probability of contribution of each pool

Description

Usage

Value

Arguments

Examples