getScaffoldsWithThisType

Getting all scaffolds classified as a specific scaffold type

Provides functions for summarizing and plotting the output of the command-line tool 'BeXY' (<https://bitbucket.org/wegmannlab/bexy>), a tool that performs Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.

Madleina Caduff

bexy

Visualize and Parse the Output of 'BeXY'

Raphael Eckel

Christoph Leuenberger

Daniel Wegmann

getScaffoldsWithThisType function

<dl><dt>object</dt>
<dd>A bexy object.</dd>
<dt>type</dt>
<dd>One specific scaffold type, can be Autosome, Y-linked, X-linked or Different.</dd>
<dt>threshold_certainty</dt>
<dd>The threshold for certainty on the posterior probabilities. All scaffolds that have a posterior probability less than this threshold are classified as 'uncertain'.</dd></dl>

Arguments

Getting all scaffolds classified as a specific scaffold type — getScaffoldsWithThisType

<dl>

<dt>object</dt>
<dd>A bexy object.</dd>


<dt>type</dt>
<dd>One specific scaffold type, can be Autosome, Y-linked, X-linked or Different.</dd>


<dt>threshold_certainty</dt>
<dd>The threshold for certainty on the posterior probabilities. All scaffolds that have a posterior probability less than this threshold are classified as 'uncertain'.</dd>

</dl>

getScaffoldsWithThisType: Getting all scaffolds classified as a specific scaffold type

Description

Usage

Value

Arguments

See Also

Examples