in R:
require(devtools)
install_github('Fraternalilab/BrepConvert', ref = 'main')
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.
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). Discovery Immunology, 2023, Volume 2, Issue 1, 2023, kyad002, https://doi.org/10.1093/discim/kyad002.