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Read a .nadia file

Source: R/Database_Read.R
read_nadia.Rd

Loads the whole analysis: the preprocessing tables, the processing results, the intensity matrices, the parameters and the provenance. The canonical tables come out of the SQL views stored in the file, with their R classes and column order restored.

Usage

read_nadia(file)

Arguments

file

Path to a .nadia file.

Value

An object of class nadia_db: a list with file, meta, parameters, calls, packages, source_files, the canonical tables (metadata, protein_id, protein_quant and, when present, DEPs_results, BoxPlot_Input, PCA_Input, pattern_profiler), the matrices and the imputed_values mask.

Details

To get objects the rest of the package can use directly, pass the result to nadia_preprocessing() or nadia_result().

See also

write_nadia(), nadia_result(), nadia_preprocessing()

Examples

if (requireNamespace("duckdb", quietly = TRUE)) {
    data(nadia_dia)
    res <- process_proteomics(nadia_dia, verbose = FALSE)
    f <- file.path(tempdir(), "read.nadia")
    write_nadia(f, nadia_dia, res, verbose = FALSE)

    db <- read_nadia(f)
    db
    identical(db$protein_quant, nadia_dia$protein_quant)

    unlink(f)
}