genotype_statistics_cmd: Collect parameters from the command line and use them to...

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

Collect parameters from the command line and use them to create a report and CSV file

Description

Collect parameters from the command line and use them to create a report and CSV file

Usage

genotype_statistics_cmd(args = NULL)

Arguments

args	A string vector containing the command line arguments. If NULL, will take them from the command line

Value

Nothing

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(), 'repertoire.tsv')

genotype_statistics_cmd(c(
              reference_set,
              'Homosapiens',
              repfile,
              'IGHV',
              '--inf_file', inferred_set,
              '--format', 'none'))

# clean up
outfile = file.path(tempdir(), 'repertoire_ogrdb_report.csv')
plotdir = file.path(tempdir(), 'repertoire_ogrdb_plots')
file.remove(repfile)
file.remove(outfile)
unlink(plotdir, recursive=TRUE)

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