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[[organism]][[locus]][[segment]] Organism refers to species (i.e. human, mouse) 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"