preprocess_diann_anndata

Preprocess DIANN output and return AnnData

Description

Same interface as preprocess_DIANN but returns an anndataR::AnnData object instead of list(lfqdata, protein_annotation).

Usage

preprocess_DIANN_anndata(
  quant_data,
  fasta_file,
  annotation,
  pattern_contaminants = "^zz|^CON|Cont_",
  pattern_decoys = "^REV_|^rev",
  q_value = 0.01,
  hierarchy_depth = 1,
  nr_peptides = 1
)

Arguments

quant_data path to quantification data file

fasta_file path to fasta file(s)

annotation annotation list from read_annotation

pattern_contaminants regex pattern for contaminants

pattern_decoys regex pattern for decoys

q_value q-value threshold for filtering

hierarchy_depth hierarchy depth for aggregation

nr_peptides minimum number of peptides per protein

Details

The AnnData uns slot contains three namespaces:

X_layer_name: Name of the primary intensity column stored in X
exploreDE: Column role metadata compatible with anndata_omics_bridge
prolfquapp: Round-trip reconstruction metadata (config, protein annotation)

Value

anndataR::AnnData object

Examples

library("prolfquapp")

x <- get_DIANN_files("inst/application/DIANN/2706527/")
annotation <- file.path("inst/application/DIANN/2706527/dataset.csv") |>
  readr::read_csv() |>
  prolfquapp::read_annotation(QC = TRUE)
adata <- preprocess_DIANN_anndata(x$data, x$fasta, annotation)