geneUsage: Double chromosome deletion by relative gene usage

In rabhit: Inference Tool for Antibody Haplotype

Double chromosome deletion by relative gene usage

Description

The geneUsage function calculates the relative gene usage.

Usage

geneUsage(
  clip_db,
  chain = c("IGH", "IGK", "IGL", "TRB"),
  genes_order = NULL,
  rmPseudo = TRUE
)

Arguments

clip_db	a data.frame in AIRR format. See details.
chain	the IG/TR chain: IGH,IGK,IGL,TRB. Default is IGH.
genes_order	A vector of the genes by the desired order. Default is by GENE.loc
rmPseudo	if TRUE non-functional and pseudo genes are removed. Default is TRUE.

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)

Value

A data.frame, in which each row is the relative gene usage value per individual.

The output containes the following columns:

• subject: the subject name.

• gene: the gene call

• frac: the relative gene usage of the gene

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