rabhit (version 0.2.5)

deletionsByBinom: Double chromosome deletion by relative gene usage

Description

The deletionsByBinom function inferes double chromosome deletion events by relative gene usage.

Usage

deletionsByBinom(
  clip_db,
  chain = c("IGH", "IGK", "IGL"),
  nonReliable_Vgenes = c(),
  genes_order = NULL
)

Value

A data.frame, in which each row is the double chomosome deletion inference of a gene.

The output containes the following columns:

• subject: the subject name.

• gene: the gene call

• frac: the relative gene usage of the gene

• cutoff: the the cutoff of for the binomial test

• pval: the p-value of the binomial test

• deletion: if a double chromosome deletion event of a gene occured.

Arguments

clip_db

a data.frame in AIRR format. See details.

chain

the IG/TR chain: IGH,IGK,IGL,TRB. Default is IGH.

nonReliable_Vgenes

a list of known non reliable gene assignments. A list created by nonReliableVGenes.

genes_order

A vector of the genes by the desired order. Default is by GENE.loc

Details

The function accepts a data.frame in AIRR format (https://changeo.readthedocs.io/en/stable/standard.html) containing the following columns:

• 'subject': The subject name

• 'v_call': V allele call(s) (in an IMGT format)

• 'd_call': D allele call(s) (in an IMGT format, only for heavy chains)

• 'j_call': J allele call(s) (in an IMGT format)

Examples

# Load example data and germlines
data(samples_db)

# Selecting a single individual
clip_db = samples_db[samples_db$subject=='I5', ]
# Infering haplotype
del_binom_df = deletionsByBinom(clip_db)
head(del_binom_df)