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Differential abundance with clusters, from a .nadia file

Source: R/Database_Read.R
nadia_deps_with_clusters.Rd

The file's own answer to deps_with_clusters(). The join lives in the file as the view v_deps_pattern_profiler, so this reads a table rather than building one, and a client that is not R gets the same table from the same SQL. The filters are the ones deps_with_clusters() applies, and the two functions return identical results for the same arguments.

Usage

nadia_deps_with_clusters(
  db,
  assignment = c("primary", "all"),
  min_membership = NULL,
  comparison = NULL,
  significant_only = FALSE
)

Arguments

db

A nadia_db from read_nadia(), or the path to a .nadia file.

assignment

"primary" (default) for one row per protein and comparison, carrying the cluster of highest membership; "all" for one row per protein, comparison and cluster.

min_membership

Optional extra membership threshold. It can only be stricter than the one the analysis ran with.

comparison

Optional character vector of comparisons to keep.

significant_only

Keep only the rows classified Up or Down.

Value

A data frame with the columns of DEPs_results followed by Cluster, Membership and ClusterRank, or NULL if the file holds no differential-abundance results. A file with results but no clustering returns the same shape with the three cluster columns NA.

Details

The table is read on demand rather than by read_nadia(), because it is as long as the number of proteins times comparisons times clusters and there is no reason to carry it around unasked.

See also

deps_with_clusters(), nadia_add_pattern_profiler()

Examples

if (requireNamespace("duckdb", quietly = TRUE)) {
    data(nadia_dia)
    res <- process_proteomics(nadia_dia, verbose = FALSE)

    f <- file.path(tempdir(), "functional.nadia")
    write_nadia(f, nadia_dia, res, verbose = FALSE)

    head(nadia_deps_with_clusters(f))

    unlink(f)
}
#> Warning: 'functional.nadia' holds no Pattern Profiler view: the cluster columns are all NA. Add a clustering with nadia_add_pattern_profiler().