Convert LFQData + ProteinAnnotation to AnnData with round-trip metadata

Description

Builds an AnnData object from LFQData and ProteinAnnotation, with the prolfquapp uns namespace for lossless round-trip via LFQData_from_anndata.

Usage

preprocess_anndata_from_lfq(lfqdata, protAnnot, source_software = "unknown")

Arguments

lfqdata	LFQData object
protAnnot	ProteinAnnotation object
source_software	character, name of the source software (e.g. "DIANN")

Details

Handles both protein-level (hierarchyDepth=1) and peptide-level (hierarchyDepth=2) data. For peptide-level data, var contains one row per feature (peptide) with protein annotation joined in.

Value

anndataR::AnnData object

Examples

library("prolfquapp")

if (requireNamespace("anndataR", quietly = TRUE)) {
  # Protein-level
  res <- sim_data_protAnnot(Nprot = 10, PROTEIN = TRUE)
  adata <- preprocess_anndata_from_lfq(res$lfqdata, res$pannot, "simulated")
  adata  # 12 obs x 10 var

  # Peptide-level (multiple peptides per protein)
  res2 <- sim_data_protAnnot(Nprot = 10, PROTEIN = FALSE)
  adata2 <- preprocess_anndata_from_lfq(res2$lfqdata, res2$pannot, "simulated")
  adata2  # 12 obs x ~28 var (peptides)

  # Round-trip back to LFQData
  back <- LFQData_from_anndata(adata2)
  back$lfqdata$hierarchy_counts()
}

# A tibble: 1 × 3
  isotopeLabel protein_Id peptide_Id
  <chr>             <int>      <int>
1 light                10         28