plotDeletionsByBinom: Graphical output of double chromosome deletions

In rabhit: Inference Tool for Antibody Haplotype

Graphical output of double chromosome deletions

Description

The plotDeletionsByBinom function generates a graphical output of the double chromosome deletions in multiple samples.

Usage

plotDeletionsByBinom(
  GENE.usage.df,
  chain = c("IGH", "IGK", "IGL", "TRB", "TRA"),
  genes.low.cer = c("IGHV3-43", "IGHV3-20"),
  genes.dup = c("IGHD4-11", "IGHD5-18"),
  genes_order = NULL
)

Arguments

GENE.usage.df	double chromosome deletion summary table. See details.
chain	the IG chain: IGH,IGK,IGL. Default is IGH.
genes.low.cer	a vector of IGH genes known to be with low certantiny in the binomial test. Default is IGHV3-43 and IGHV3-20
genes.dup	a vector of IGH genes known to have a duplicated gene. Default is IGHD4-11 that his duplicate is IGHD4-4 and IGHD5-18 that his duplicate is IGHD5-5
genes_order	A vector of the genes by the desired order. Default is by GENE.loc

Details

A data.frame created by binom_test_deletion.

Value

A double chromosome deletion visualization.

Examples

# Load example data and germlines
data(samples_db)

# Infering haplotype
deletions_db = deletionsByBinom(samples_db);
plotDeletionsByBinom(deletions_db)

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