Process JAFFA gene fusion fasta and results.csv output for neoantigen prediction using garnish_affinity.

garnish_jaffa(path, db, fasta_path)

Arguments

path

Path to jaffa_results.csv.

db

One of "GRCm38" or "GRCh38", murine and human reference genomes respectively.

fasta_path

Path to jaffa_results.fasta.

Value

A data table of mutant peptides, including:

  • sample_id: sample id

  • pep_mut: mutant fusion peptide

  • mutant_index: index of mutant peptide

  • fusion gene: colon-separated gene names for the fusion product

  • chrom1: chromosome of first fusion gene

  • base1: base number of first fusion gene breakpoint

  • chrom2: chromosome of second fusion gene

  • base2: base number of second fusion gene breakpoint

  • fusion_uuid: unique identifier

  • pep_wt: wt cDNA sequence of peptide from 5' fusion gene.

  • fus_tx: cDNA sequence of predicted fusion product

See also

Examples

if (FALSE) { library(magrittr) library(antigen.garnish) # load example jaffa output dir <- system.file(package = "antigen.garnish") %>% file.path(., "extdata/testdata") path <- "antigen.garnish_jaffa_results.csv" %>% file.path(dir, .) fasta_path <- "antigen.garnish_jaffa_results.fasta" %>% file.path(dir, .) # get predictions dt <- garnish_jaffa(path, db = "GRCm38", fasta_path) %>% # add MHC info with list_mhc() compatible names .[, MHC := "H-2-Kb"] %>% # get predictions garnish_affinity %>% # summarize predictions garnish_summary %T>% print }