Read an APB result

Description

Reads a result apb2 wrote into a ParsedLevels object, one anndataR AnnData per level, the same for every format: a .h5ad file, a .duckdb file, or the directory apb2 writes for a .parquet result. Reading Parquet needs the arrow package, DuckDB the duckdb and DBI packages; .h5ad needs nothing beyond anndataR.

Usage

read_parsed_levels(path)

Arguments

path	The result, such as converted.h5ad, converted.duckdb or the directory converted.parquet.

Value

A ParsedLevels object.

Examples

library("apbCatalogR")

results <- tempfile()
archive <- system.file(
    "extdata", "test-bundle", "results.tar.gz",
    package = "apbCatalogR"
)
utils::untar(archive, exdir = results)
read_parsed_levels(file.path(results, "edge-two-levels.parquet"))

<ParsedLevels>
  peptidoform_ion: 2 x 3, layers: Ms1_Normalised, Precursor_Normalised, Precursor_Quantity, Ms1_Area, Q_Value, PEP, RT, Averagine, Best_Fr_Mz, Best_Fr_Mz_Delta, Channel_Evidence, Channel_Q_Value, Empirical_Quality, Evidence, FWHM, GG_Q_Value, IM, Mass_Evidence, Ms1_Apex_Area, Ms1_Apex_Mz_Delta, Ms1_Profile_Corr, Ms1_Q_Value, Ms1_Total_Signal_After, Ms1_Total_Signal_Before, Normalisation_Factor, Normalisation_Noise, PTM_Site_Confidence, Peptidoform_Q_Value, Predicted_IM, Predicted_RT, Predicted_iIM, Predicted_iRT, Profile_After, Profile_Before, Profile_HM, Protein_Q_Value, Quantity_Quality, RT_Start, RT_Stop, Translated_Q_Value
  protein: 2 x 3, layers: PG_MaxLFQ, Genes_MaxLFQ, PG_Q_Value, PG_PEP, Genes_MaxLFQ_Empirical_Quality, Genes_MaxLFQ_Empirical_Unique_Quality, Genes_MaxLFQ_Quality, Genes_MaxLFQ_Unique, Genes_MaxLFQ_Unique_Quality, Genes_TopN, PG_MaxLFQ_Empirical_Quality, PG_MaxLFQ_Quality, PG_TopN