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Create lookup tables

Source: R/build_lookup.R
build_lookup_from_fastas.Rd

build_lookup_from_fastas() processes IMGT reference FASTA files in a given folder to generate lookup tables used for making gene name conversions. It extracts all gene names and transforms them into 10X and Adaptive formats following predefined conversion rules. The resulting files are created:

  • lookup.csv: IMGT gene names and their 10X and Adaptive equivalents.

  • lookup_from_tenx.csv: Gene names aggregated by their 10X identifiers, with one representative allele (*01) for each.

  • lookup_from_adaptive.csv: Adaptive gene names, with or without alleles and gene designations, and their IMGT and 10X equivalents.

The files are stored in a given subfolder (species) within the appropriate application folder via rappdirs. For example:

  • MacOS: ~/Library/Application Support/<AppName>

  • Windows: C:\Documents and Settings\<User>\Application Data\Local Settings\<AppAuthor>\<AppName>

  • Linux: ~/.local/share/<AppName>

If a folder named species already exists in that location, it will be replaced.

Usage

build_lookup_from_fastas(data_dir, species)

Arguments

data_dir

A string, the directory containing FASTA files.

species

A string, the name of species that will be used when running TCRconvert with these lookup tables.

Value

A string, path to new lookup directory

Details

Key transformations from IMGT:

  • 10X:

    • Remove allele information (e.g., *01) and modify /DV occurrences.

  • Adaptive:

    • Apply renaming rules, such as adding gene-level designations and zero-padding single-digit numbers.

    • Convert constant genes to "NoData" (Adaptive only captures VDJ) which become NA after the merge in convert_gene().

Examples

# For the example, create and use a temporary folder
fastadir <- file.path(tempdir(), "TCRconvertR_tmp")
dir.create(fastadir, showWarnings = FALSE, recursive = TRUE)
trav <- get_example_path("fasta_dir/test_trav.fa")
trbv <- get_example_path("fasta_dir/test_trbv.fa")
file.copy(c(trav, trbv), fastadir)
#> [1] TRUE TRUE

# Build lookup tables
build_lookup_from_fastas(fastadir, "rabbit")
#> Writing lookup tables to: ~/.local/share/TCRconvertR/rabbit
#> [1] "~/.local/share/TCRconvertR/rabbit"

# Clean up temporary folder
unlink(fastadir, recursive = TRUE)