readIMGT read in IMGT database
Loads all reference germlines from an Immcantation-formatted IMGT database.
readIMGT(dir, quiet = FALSE)
- directory containing Immcantation-formatted IMGT database
- print warnings?
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)
Input directory must be formatted to Immcantation standard. See https://changeo.readthedocs.io/en/stable/examples/igblast.html for example of how to download.
# 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)
 "Read in 3 from 3 fasta files"