rabhit: The RAbHIT package

In rabhit: Inference Tool for Antibody Haplotype

The RAbHIT package

Description

The rabhit package provides a robust novel method for determining antibody heavy and light chain haplotypes by adapting a Bayesian framework. The key functions in rabhit, broken down by topic, are described below.

Haplotype and deletions inference

rabhit provides tools to infer haplotypes based on given anchor genes, deletion detection based on relative gene usage, pooling v genes, and a single anchor gene.

• createFullHaplotype: Haplotypes inference and single chromosome deletions based on an anchor gene.

• deletionsByVpooled: Single chromosomal deletion detection by pooling V genes.

• deletionsByBinom: Double chromosomal deletion detection by relative gene usage.

• geneUsage: Relative gene usage.

• nonReliableVGenes: Non reliable gene assignment detection.

Haplotype and deletions visualization

Functions for visualization of the inferred haplotypes and deletions

• plotHaplotype: Haplotype inference map.

• deletionHeatmap: Single chromosome deletions heatmap.

• hapHeatmap: Chromosome comparison of multiple samples.

• hapDendo: Hierarchical clustering of multiple haplotypes based on Jaccard distance.

• plotDeletionsByVpooled: V pooled based single chromosome deletions heatmap.

• plotDeletionsByBinom: Double chromosome deletions heatmap.

References

1. Gidoni, M., Snir, O., Peres, A., Polak, P., Lindeman, I., Mikocziova, I., . . . Yaari, G. (2019). Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping. Nature Communications, 10(1). doi:10.1038/s41467-019-08489-3

rabhit documentation built on Feb. 16, 2023, 9:25 p.m.