compute_linkage_groups

This is a function to compute the conserved linkage groups shared between two or more species.
It computes the significant associations between chromosomes of all species versus all (pairwise)
using the fischer test implemented in compute_macrosynteny().
It outputs a dataframe shaped as following :
sp1.Chr,sp2.Chr,..., spN.chr,n,LGs
where n is the number of shared orthologs in the group and LGs are the IDs for the linkage groups

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

compute_linkage_groups function

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

Arguments

Compute Linkage groups — compute_linkage_groups

<dl>

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

</dl>

compute_linkage_groups: Compute Linkage groups

Description

Usage

Value

Arguments

Examples