# Inference Tool for Antibody Haplotype

## Documentation for package ‘rabhit’ version 0.4.0

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

## Help Pages

.onAttach | .onAttach start message
convertToASC | Prepare AIRR-seq data and germline for haplotype inference with allele similarity clusters (ASC)
createFullHaplotype | Anchor gene haplotype inference
createHaplotypeTable | Create haplotype table
deletionHeatmap | Graphical output of single chromosome deletions
deletionsByBinom | Double chromosome deletion by relative gene usage
deletionsByVpooled | Single chromosomal D or J gene deletions inferred by the V pooled method
GENE.loc | Human Gene order on the chromosome
geneUsage | Double chromosome deletion by relative gene usage
GERM | Human germlines
hapDendo | Hierarchical clustering of haplotypes graphical output
hapHeatmap | Graphical output of alleles division by chromosome
HDGERM | Human IGHD germlines
HJGERM | Human IGHJ germlines
HVGERM | Human IGHV germlines
KJGERM | Human IGKJ germlines
KVGERM | Human IGKV germlines
LJGERM | Human IGLJ germlines
LVGERM | Human IGKV germlines
nonReliableVGenes | Detect non reliable gene assignment
plotDeletionsByBinom | Graphical output of double chromosome deletions
plotDeletionsByVpooled | Graphical output for single chromosome D or J gene deletions according to V pooled method
plotHaplotype | Graphical output of an inferred haplotype
rabhit | The RAbHIT package
readHaplotypeDb | Read a Change-O tab-delimited database file
samplesHaplotype | Example haplotype inference results
samples_db | Example IGH human naive b-cell repertiore