nonReliableVGenes: Detect non reliable gene assignment
In rabhit: Inference Tool for Antibody Haplotype

nonReliableVGenes

R Documentation

Detect non reliable gene assignment

Description

nonReliableVGenes Takes a data.frame in AIRR format and detect non reliable IGHV genes. A non reliable gene is when the ratio of the multiple assignments with a gene is below the threshold.

Usage

nonReliableVGenes(clip_db, thresh = 0.9, appearance = 0.01)

Arguments

`clip_db`	a `data.frame` in AIRR format. See details.
`thresh`	the threshold to consider non reliable gene. Default is 0.9
`appearance`	the minimum fraction of gene appearance to be considered for reliability check. Default is 0.01.

Details

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

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

Value

a nested list of non reliable genes for all subject.

Examples

# Example IGHV call data frame
clip_db <- data.frame(subject=rep('S1',6),
v_call=c('IGHV1-69*01','IGHV1-69*01','IGHV1-69*01,IGHV1-69*02',
'IGHV4-59*01,IGHV4-61*01','IGHV4-59*01,IGHV4-31*02','IGHV4-59*01'))
# Detect non reliable genes
nonReliableVGenes(clip_db)

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