MergeIdenticalHaplotypes

If any alleles within a locus have identical <code>alleleNucleotides</code> values
(including those identical based on IUPAC ambiguity codes),
this function merges those alleles, summing their read depths. This function is
primarily intended to be used internally in cases where tags vary in length
within a locus, resulting in truncated <code>alleleNucleotides</code>.

 manip 

Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids. The genotype
probabilities, posterior mean genotypes, or most probable genotypes can then
be exported for downstream analysis. 'polyRAD' is described by Clark et al.
(2019) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker
filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>.
A variant calling pipeline for highly duplicated genomes is also included and
is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.

Lindsay V. Clark

polyRAD

Genotype Calling with Uncertainty from Sequencing Data in
Polyploids and Diploids

U.S. National Science Foundation 

MergeIdenticalHaplotypes function

<dl> <dt>object</dt>
<dd>A <code>RADdata</code> object.</dd> <dt>...</dt>
<dd>Additional arguments (none implemented).</dd></dl>

Arguments

Author

Merge Alleles with Identical DNA Sequences — MergeIdenticalHaplotypes

<dl>

 <dt>object</dt>
<dd>A <code>RADdata</code> object.</dd>

 <dt>...</dt>
<dd>Additional arguments (none implemented).</dd>

</dl>

MergeIdenticalHaplotypes: Merge Alleles with Identical DNA Sequences

Description

Usage

Value

Arguments

Author

See Also

Examples