Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes

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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