Package index • paneffectR

Loading Data

Functions for loading protein sequences and effector prediction scores from FASTA files and omnieff output.

load_proteins(): Load proteins from multiple assemblies
load_fasta(): Load a single FASTA file
load_scores(): Load effector scores from CSV
load_name_mapping(): Load name mapping from CSV

Creating Objects

Constructors for the core S3 classes used throughout the package.

new_protein_set(): Create a protein_set object
new_protein_collection(): Create a protein_collection object
new_orthogroup_result(): Create an orthogroup_result object
new_pa_matrix(): Create a pa_matrix object

Clustering

Functions for clustering proteins into orthogroups using sequence similarity.

cluster_proteins(): Cluster proteins across assemblies

Matrix Building

Build presence/absence matrices from clustering results.

build_pa_matrix(): Build presence/absence matrix from clustering results
filter_by_score(): Filter presence/absence matrix by score
`[`(<pa_matrix>): Subset a pa_matrix object
as.data.frame(<pa_matrix>): Convert pa_matrix to data.frame

Singletons

Functions for working with unclustered proteins (singletons).

get_singletons(): Get singletons from clustering result
n_singletons(): Count singletons
singletons_by_assembly(): Summarize singletons by assembly

Visualization

Publication-ready plots for exploring presence/absence patterns.

plot_heatmap(): Plot presence/absence heatmap
plot_upset(): Plot UpSet diagram of orthogroup sharing
plot_scores(): Plot effector score distributions
plot_dendro(): Plot assembly clustering dendrogram
plot_pan_structure(): Plot pan-genome structure
plot_assembly_composition(): Plot assembly composition

Utilities

Helper functions for external tool management.

check_tool_installed(): Check if an external tool is installed
find_tool(): Find an external tool