rabhit (version 0.2.5)

plotDeletionsByBinom: 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
)

Value

A double chromosome deletion visualization.

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.

Examples

# Load example data and germlines
data(samples_db)

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