Alakazam: How to read and write files

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

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 Immcantation v4.0.0, which corresponds to alakazam v1.0.0.

Reading data

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.

# Set the file paths from inside the package directory
# These files are smaller versions of the example databases previously mentioned
changeo_file <- system.file("extdata", "example_changeo.tab.gz", package="alakazam")
airr_file <- system.file("extdata", "example_airr.tsv.gz", package="alakazam")

# Read in the data
db_changeo <- alakazam::readChangeoDb(changeo_file)
db_airr <- airr::read_rearrangement(airr_file)

Writing data

# Write the data to a tab-delimited file
alakazam::writeChangeoDb(db_changeo, "changeo.tsv")
airr::write_rearrangement(db_airr, "airr.tsv")

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.