Examples/ExampleComparisonUsingPartis.R

In matsengrp/sumrep: Summary statistics for B cell receptor (BCR) repertoires

# The path of the sumrep directory. This will need to be changed if the sumrep
#   directory is not the working directory.
path_to_sumrep <- getwd()

# Make sure sumrep is loaded
devtools::load_all(path_to_sumrep)

# Get annnotation and clonal partition dataset for IgH sequences
test_dat <- getPartisAnnotations(system.file("extdata", "test_data.fa", package="sumrep"),
                                 locus="igh",
                                 cleanup=FALSE,
                                 output_path="tmp_output")

# Simulate a dataset based on the observed DNA sequences
test_simu <- getPartisSimulation(parameter_dir="tmp_output",
                                 num_events=nrow(test_dat[["annotations"]]),
                                 seed=123,
                                 extra_command_args="--min-observations-per-gene 1")
                                 # ^ partis has troubles simulating from small
                                 # datasets, so give it some wiggle room

# Delete partis output folder
"tmp_output" %>% unlink(recursive=TRUE)

# Run repertoire comparison for the observed and simulated data,
# and also compare the observed to bootstrapped data for refernce
comparison <- compareRepertoires(test_dat, 
                                 test_simu, 
                                 locus="igh")