ogrdbstats (version 0.5.4)

generate_ogrdb_report: 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 = ""
)

Value

None

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

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)