generate_ogrdb_report: Generate OGRDB reports from specified files.

In airr-community/ogrdbstats: Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics

Generate OGRDB reports from specified files.

Description

This creates the genotype report (suffixed _ogrdb_report.csv) and the plot file (suffixed _ogrdb_plos.pdf). Both are created in the directory holding the annotated read file, and the file names are prefixed by the name of the annotated read file.

Usage

generate_ogrdb_report(
  ref_filename,
  inferred_filename,
  species,
  filename,
  chain,
  hap_gene,
  segment,
  chain_type,
  plot_unmutated,
  all_inferred = FALSE,
  format = "pdf",
  custom_file_prefix = ""
)

Arguments

ref_filename	Name of file containing IMGT-aligned reference genes in FASTA format
inferred_filename	Name of file containing sequences of inferred novel alleles, or '-' if none
species	Species name used in field 3 of the IMGT germline header with spaces omitted, if the reference file is from IMGT. Otherwise ”
filename	Name of file containing annotated reads in AIRR, CHANGEO or IgDiscover format. The format is detected automatically
chain	one of IGHV, IGKV, IGLV, IGHD, IGHJ, IGKJ, IGLJ, TRAV, TRAj, TRBV, TRBD, TRBJ, TRGV, TRGj, TRDV, TRDD, TRDJ
hap_gene	The haplotyping columns will be completed based on the usage of the two most frequent alleles of this gene. If NA, the column will be blank
segment	one of V, D, J
chain_type	one of H, L
plot_unmutated	Plot base composition using only unmutated sequences (V-chains only)
all_inferred	Treat all alleles as novel
format	The format for the plot file ('pdf', 'html' or 'none')
custom_file_prefix	custom prefix to use for output files. If not specified, the prefix is taken from the input file name

Value

None

Examples

# prepare files for example
reference_set = system.file("extdata/ref_gapped.fasta", package = "ogrdbstats")
inferred_set = system.file("extdata/novel_gapped.fasta", package = "ogrdbstats")
repertoire = system.file("extdata/ogrdbstats_example_repertoire.tsv", package = "ogrdbstats")
file.copy(repertoire, tempdir())
repfile = file.path(tempdir(), 'ogrdbstats_example_repertoire.tsv')

generate_ogrdb_report(reference_set, inferred_set, 'Homosapiens',
          repfile, 'IGHV', NA, 'V', 'H', FALSE, format='none')

#clean up
outfile = file.path(tempdir(), 'ogrdbstats_example_repertoire_ogrdb_report.csv')
file.remove(repfile)
file.remove(outfile)

airr-community/ogrdbstats documentation built on Feb. 17, 2025, 5:05 p.m.