As part of the Immcantation suite of tools, the alakazam package includes a set of built-in functions capable of reading and writing tab-delimited database files created by Change-O into R data.frames. However, due to differences in how certain values and sequences are handled, alakazam::readChangeoDb and alakazam::writeChangeoDb will not properly read in AIRR formatted files. These files should instead be loaded using the functions included in the airr package (airr::read_rearrangement and airr::write_rearrangement).
You can read more about how we use both data standards here and here. Please note that the default file format for all functions in Immcantation is the AIRR-C format as of release 4.0.0.
Small example databases for both the Change-O format (ExampleDbChangeo) and the AIRR format (ExampleDb) are included in the alakazam package. For specific details about the latter, visit the AIRR Community documentation site.
# Load required packages
library(airr)
library(alakazam)
# Read in the data
db_changeo <- readChangeoDb("../data-raw/ExampleDbChangeo.gz")
db_airr <- read_rearrangement("../data-raw/ExampleDb.gz")
# Write the data to a tab-delimited file
writeChangeoDb(db_changeo, "changeo.tsv")
write_rearrangement(db_airr, "airr.tsv")