get_syntenic_genes

This is a function to extract all the syntenic genes from an orthologs_df. It requires as input an orthologs_df loaded by load_orthologs().

Use standard genomics file format (BED) and a table of orthologs to
illustrate synteny conservation at the genome-wide scale.
Significantly conserved linkage groups are identified as described in Simakov et al. (2020) <doi:10.1038/s41559-020-1156-z>
and displayed on an Oxford Grid (Edwards (1991) <doi:10.1111/j.1469-1809.1991.tb00394.x>) or a chord diagram as in Simakov et al. (2022) <doi:10.1126/sciadv.abi5884>.
The package provides a function that uses a network-based greedy algorithm to find communities (Clauset et al. (2004) <doi:10.1103/PhysRevE.70.066111>)
and so automatically order the chromosomes on the plot to improve interpretability.

Sami El Hilali

macrosyntR

Draw Ordered Oxford Grids and Chord Diagrams

Richard Copley

get_syntenic_genes function

<dl><dt>orthologs_df</dt>
<dd>dataframe. orthologs with genomic coordinates loaded by load_orthologs()</dd></dl>

Arguments

get the syntenic genes as a table — get_syntenic_genes

<dl>

<dt>orthologs_df</dt>
<dd>dataframe. orthologs with genomic coordinates loaded by load_orthologs()</dd>

</dl>

get_syntenic_genes: get the syntenic genes as a table

Description

Usage

Value

Arguments

See Also

Examples