README.md

In Fraternalilab/BrepConvert: BrepConvert: R package for gene conversion analysis of B cell repertoire

BrepConvert

R package to analyse gene conversion events in immunoglobulin sequences.

Install

in R:

require(devtools)
install_github('Fraternalilab/BrepConvert', ref = 'main')

How to use

This vignette contains examples on how to use BrepConvert.

The analysis performed on Mallaby et al. was performed as follows: IMGT-gapped V gene sequences were splitted into batches of 3000 sequences, each read into R as a named vector. One of these files is uploaded here in the directory example.

The following shows the run-code to generate the result of this file via BrepConvert:

library(Biostrings)
library(BrepConvert)

sequences <- readDNAStringSet("MallabyEtAl_example_set.fasta")
functional_IGHV <- "IGHV_functional_gapped.fasta" # Downloads 21/08/2020
pseudogene_IGHV <- "IGHV_Pseudogenes_gapped.fasta"

blat <- system.file("exe/blat", package = "BrepConvert")

annotation <- batchConvertAnalysis(
  functional = functional_IGHV,
  pseudogene = pseudogene_IGHV,
  repertoire = sequences,
  blat_exec = blat
)

The corresponding output file (in CSV format) is also uploaded into the example directory in this repository.

Cite

Mallaby J, Ng JCF, Stewart AS, Sinclair E, Dunn-Walters DK, Hershberg U. Diversification of Antibodies by Gene Conversion in the Domestic Chicken (Gallus gallus domesticus). Under Review.

Fraternalilab/BrepConvert documentation built on Oct. 14, 2022, 5:54 p.m.