rabhit (version 0.2.5)

nonReliableVGenes: 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)

Value

a nested list of non reliable genes for all subject.

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)

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)