rabhit | R Documentation |
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.
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.
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.
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
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