readIMGT - readIMGT read in IMGT database

Description¶

Loads all reference germlines from an Immcantation-formatted IMGT database.

Usage¶

readIMGT(dir, quiet = FALSE)

Arguments¶

dir

directory containing Immcantation-formatted IMGT database

quiet

print warnings?

Value¶

List of lists, leading to IMGT-gapped nucleotide sequences. Structure of object is list[[locus]][[segment]] locus refers to locus (e.g. IGH, IGK, TRA) segment refers to gene segment caegory (V, D, or J)

Details¶

Input directory must be formatted to Immcantation standard. See https://changeo.readthedocs.io/en/stable/examples/igblast.html for example of how to download.

Examples¶

# vdj_dir contains a minimal example of reference germlines 
# (IGHV3-11*05, IGHD3-10*01 and IGHJ5*02)
# which are the gene assignments for ExamapleDb[1,]
vdj_dir <- system.file("extdata", "germlines", "imgt", "human", "vdj", package="dowser")
imgt <- readIMGT(vdj_dir)

[1] "Read in 3 from 3 fasta files"