coincidents: Find coincidents gene/proteins (clustering)
In irycisBioinfo/PATO: Pangenome Analysis Toolkit
coincidents R Documentation
Find coincidents gene/proteins (clustering)
Description
This function find groups of coincidents genes/proteins in an accnet
object. Unlike accnet_enrichment_analysis() concidents does not need
to define genome/pangenome clusters. The methos perform a multi-dimensional scaling
using umap and then find clusters with hdbscan.
Usage
coincidents(data, min_freq = 5, min_size = 4)
Arguments
data
An accnet object
min_freq
Minimun frequency of gene/protein in the population.
min_size
Minimun size of the reported clusters.
Value
A data.frame with the protein/gene ID ("Target") and the membership (cluster number)
irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.
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| coincidents | R Documentation |
Find coincidents gene/proteins (clustering)
Description
This function find groups of coincidents genes/proteins in an accnet object. Unlike accnet_enrichment_analysis() concidents does not need to define genome/pangenome clusters. The methos perform a multi-dimensional scaling using umap and then find clusters with hdbscan.
Usage
coincidents(data, min_freq = 5, min_size = 4)
Arguments
data |
An accnet object |
min_freq |
Minimun frequency of gene/protein in the population. |
min_size |
Minimun size of the reported clusters. |
Value
A data.frame with the protein/gene ID ("Target") and the membership (cluster number)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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