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One APB result: its levels on one observation axis

Description

The R counterpart of apb2’s ParsedLevels, as read_parsed_levels() returns it.

Each level is an anndataR AnnData laid out as apb2’s .h5ad writer lays it out: the primary layer in X, the other layers in layers, obs and var frames named by their key columns, and the level’s APB part in uns$apb: parse (with provenance$rule_json), roles, storage and post-parse records.

Value

The class generator; ParsedLevels$new() returns a ParsedLevels object.

Public fields

levels
A named list of anndataR AnnData, one per level.
uns
The root parse record.
metadata
The root post-parse records, such as sdrf or fasta.
hierarchy
How the levels nest, or NULL.
annotation_tables
A named list of data frames; each carries its metadata as the attribute apb.
feature_relations
A named list of data frames of source, row, target, column and value; each carries its metadata as the attribute apb.

Methods

Public methods

ParsedLevels$new()

Collect the levels and records of one result.

Usage 
ParsedLevels\$new(
  levels,
  uns = list(),
  metadata = list(),
  hierarchy = NULL,
  annotation_tables = list(),
  feature_relations = list()
)
Arguments
levels
A named list of anndataR AnnData.
uns
The root parse record.
metadata
The root post-parse records.
hierarchy
How the levels nest, or NULL.
annotation_tables
A named list of data frames.
feature_relations
A named list of data frames.

ParsedLevels$print()

Print the levels and their shapes.

Usage 
ParsedLevels\$print(...)
Arguments
…
Ignored.

ParsedLevels$clone()

The objects of this class are cloneable with this method.

Usage 
ParsedLevels\$clone(deep = FALSE)
Arguments
deep
Whether to make a deep clone.

Examples

library("apbCatalogR")

results <- tempfile()
archive <- system.file(
    "extdata", "test-bundle", "results.tar.gz",
    package = "apbCatalogR"
)
utils::untar(archive, exdir = results)
result <- read_parsed_levels(file.path(results, "edge-two-levels.parquet"))
names(result$levels)
[1] "peptidoform_ion" "protein"        
result$levels$protein
InMemoryAnnData object with n_obs × n_vars = 2 × 3
    obs: 'Run', 'Run_Index'
    var: 'Protein_Group', 'Decoy', 'Protein_Names', 'Genes', 'Lib_PG_Q_Value', 'Global_PG_Q_Value', 'apb_Decoy', 'apb_Contaminant'
    uns: 'apb'
    layers: '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'