nonReliableVGenes: Detect non reliable gene assignment

Description Usage Arguments Details Value Examples

View source: R/functions.R

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

1
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. Defualt is 0.9

appearance

the minimun fraction of gene appearance to be considered for reliability check. Defualt 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:

Value

a nested list of non reliable genes for all subject.

Examples

1
2
3
4
5
6
# 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 July 12, 2020, 1:06 a.m.