error_minimize2

This function tunes the final fitting for heterozygous genomes by adjusting the delta values for heterozygous and homozygous regions.

Provides tools to estimate the genome size of polyploid species using k-mer frequencies. This package includes functions to process k-mer frequency data and perform genome size estimation by fitting k-mer frequencies with a normal distribution model. It supports handling of complex polyploid genomes and offers various options for customizing the estimation process. The basic method 'findGSE' is detailed in Sun, Hequan, et al. (2018) <doi:10.1093/bioinformatics/btx637>.

Laiyi Fu

findGSEP

Estimate Genome Size of Polyploid Species Using k-Mer
Frequencies

error_minimize2 function

<dl><dt>tooptimize</dt>
<dd>A numeric vector containing the scale factors to optimize.</dd>
<dt>h_het</dt>
<dd>A numeric vector representing the raw fitting for the heterozygous region.</dd>
<dt>h_hom</dt>
<dd>A numeric vector representing the raw fitting for the homozygous region.</dd>
<dt>h_target</dt>
<dd>A numeric vector representing the target k-mer frequency.</dd></dl>

Arguments

Tuning Final Fitting for Heterozygous Genomes — error_minimize2

<dl>

<dt>tooptimize</dt>
<dd>A numeric vector containing the scale factors to optimize.</dd>


<dt>h_het</dt>
<dd>A numeric vector representing the raw fitting for the heterozygous region.</dd>


<dt>h_hom</dt>
<dd>A numeric vector representing the raw fitting for the homozygous region.</dd>


<dt>h_target</dt>
<dd>A numeric vector representing the target k-mer frequency.</dd>

</dl>

error_minimize2: Tuning Final Fitting for Heterozygous Genomes

Description

Usage

Value

Arguments

Examples