# Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes

## Documentation for package ‘piglet’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

alleleClusterNames | Allele similarity cluster naming scheme
allele_cluster_table | Allele similarity cluster table
allele_diff | Alleles nucleotide position difference
allele_diff_indices | Calculate differences between characters in columns of germs and return their indices as an int vector.
allele_diff_indices_parallel | Calculate SNPs or their count for each germline-input sequence pair with optional parallel execution.
allele_diff_indices_parallel2 | Calculate SNPs or their count for each germline-input sequence pair with optional parallel execution.
allele_diff_strings | Calculate differences between characters in columns of germs and return them as a string vector.
allele_threshold_table | Allele thresholds table
artificialFRW1Germline | FWR1 artificial dataset generator
assignAlleleClusters | Assign allele similarity clusters
detect_communities_leiden | Leiden community detection
distance_to_graph | Convert distance matrix to weighted graph
extractASCTable | Extracts the allele cluster table from the archive file.
generateReferenceSet | Generate allele similarity reference set
germlineASC | Converts IGHV germline set to ASC germline set.
HVGERM | Human IGHV germlines
hv_functionality | Human IGHV germlines functionality description
igClust | Allele similarity clustering
igDistance | Germline set alleles distance
ighvClust | Allele similarity clustering (deprecated)
ighvDistance | Germline set alleles distance (deprecated)
inferAlleleClusters | Allele similarity cluster
inferGenotypeAllele | Allele based genotype inference
inferGenotypeAllele_asc | Allele similarity cluster based genotype inference Testing function
insert_gaps2_vec | Insert gaps into an ungapped sequence based on a gapped reference sequence.
new_germline_cluster | Create a GermlineCluster object
optimize_resolution | Optimize resolution parameter using silhouette score
piglet | The Program for Ig clusters (PIgLET) package
plot.GermlineCluster | Plot method for GermlineCluster
plotAlleleCluster | Plotting the dendrogram of the clusters
plotClusterComparison | Compare hierarchical and Leiden clustering
plotCommunityNetwork | Plot community network
plotSilhouetteOptimization | Plot silhouette optimization results
plotTruncatedTree | Plot truncated tree visualization
print.GermlineCluster | Print method for GermlineCluster
recentAlleleClusters | Retrieving allele similarity clusters Zenodo archive
summary.GermlineCluster | Summary method for GermlineCluster
zenodoArchive | zenodoArchive