Package 'apbCatalogR'

Description

Read a var or obs slot by several keys

Usage

## S3 method for class 'Columns'
x[i, ...]

Arguments

Value

A data frame of every column the names name; the names without data.

Description

Read a slot by key

Usage

## S3 method for class 'Slot'
x[[i, ...]]

Arguments

Value

A matrix for layers, a vector for var and obs; a name without data.

Description

Answers from the catalogue alone, without data. The rule levels whose version pattern admits the version give the levels; the set's entries for that pattern give each level's fields. levels have the slots of a DataCatalog's levels, holding names: a slot answers one of the set's keys, such as "normalized_intensity", with the field's name, and its ⁠$get()⁠ takes further qualifiers, such as unit. Lookups that several fields answer, or that an unreviewed level cannot, signal UnresolvedField.

Value

The class generator; Catalog$new() returns a Catalog.

Public fields

Active bindings

Methods

Public methods

• Catalog$new()

• Catalog$fields()

• Catalog$print()

• Catalog$clone()

Catalog$new()

Bind a catalogue set to the rule levels of one software version.

Usage

Catalog$new(software, version, catalog, enforce = NULL)

Arguments

Catalog$fields()

Every catalogued field the rule declares, one row per field, as catalogue_table() shows them.

Usage

Catalog$fields()

Returns

A data frame, with present true for each row.

Catalog$print()

Print the set and the levels.

Usage

Catalog$print(...)

Arguments

Catalog$clone()

The objects of this class are cloneable with this method.

Usage

Catalog$clone(deep = FALSE)

Arguments

Examples

catalog <- Catalog$new("DIA-NN", "2.2.0", "abundance")
catalog$levels$peptidoform_ion$layers[["intensity"]]
catalog$levels$peptidoform_ion$layers$keys()

Description

Reports the bundle lookups answer from: its version, whether it was shipped with the package or downloaded by update_catalog(), and the apb2 version its rule levels come from.

Usage

catalog_version()

Value

A list with version, origin ("shipped" or "cache"), path and apb2_version.

Examples

catalog_version()

Description

One row per entry and software version it applies to, as ⁠apb-catalog table⁠ prints it.

Usage

catalogue_table(catalogue = NULL)

Arguments

Value

A data frame with columns set, source (the conversion software, an app or ⁠annotation:<convention>⁠), software_version_pattern (NA for an entry of every software version), level, location, table, name (⁠prefix:<prefix>⁠ for a field found by column-name prefix), key, kind, one ⁠qualifier.<name>⁠ column per other qualifier, requirement and entry_id.

Examples

head(catalogue_table("confidence"))

Description

Every catalogue set of the bundle with its purpose, its users and its number of entries.

Usage

catalogues()

Value

A data frame with columns catalogue, purpose, used_by (a list column), has_requirements and entries.

Examples

catalogues()

Description

Answers on a result read with read_parsed_levels() and hands the data back directly: levels give each level's slots, looked up by one of the set's keys, such as "q_value" or Sage's "quantification_q_value". Ambiguous or unreviewed answers signal UnresolvedField.

Value

The class generator; DataCatalog$new() returns a DataCatalog.

Public fields

Active bindings

Methods

Public methods

• DataCatalog$new()

• DataCatalog$fields()

• DataCatalog$print()

• DataCatalog$clone()

DataCatalog$new()

Bind catalogue sets to the levels of one result; apb, APB's own fields, is always in.

Usage

DataCatalog$new(result, ..., enforce = NULL)

Arguments

DataCatalog$fields()

Every catalogued field of the result in every composed set, one row per field, as catalogue_table() shows them.

Usage

DataCatalog$fields()

Returns

A data frame with present and, for a field apb2 left out because it held one value, that constant.

DataCatalog$print()

Print the set and the levels.

Usage

DataCatalog$print(...)

Arguments

DataCatalog$clone()

The objects of this class are cloneable with this method.

Usage

DataCatalog$clone(deep = FALSE)

Arguments

Examples

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, "maxquant_wide-peptidoform_ion.parquet")
)
catalog <- DataCatalog$new(result, "confidence")
dim(catalog$levels$peptidoform_ion$layers[["pep"]])
catalog$levels$peptidoform_ion$layers$name("pep")

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

Methods

Public methods

• ParsedLevels$new()

• ParsedLevels$print()

• ParsedLevels$clone()

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

ParsedLevels$print()

Print the levels and their shapes.

Usage

ParsedLevels$print(...)

Arguments

ParsedLevels$clone()

The objects of this class are cloneable with this method.

Usage

ParsedLevels$clone(deep = FALSE)

Arguments

Examples

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$levels)
result$levels$protein

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

Value

A ParsedLevels object.

Examples

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"))

Description

One row per catalogued or required field of each rule level the set reviews; a set without vendor catalogues is checked against every level the bundle's entries name for each version of versions.csv. A set with requirements judges each level: fail when a MUST field is unsupported, warn when a SHOULD or MAY field is, pass otherwise.

Usage

rule_coverage(catalogue)

Arguments

Value

A data frame with columns software, version (the label), software_version_pattern, level, key, kind, qualifiers (the other qualifiers as name=value), origin, producer (the app, NA for the conversion software's fields), requirement, location, table, column (NA when unsupported), needs (what to run before the field exists) and verdict (NA for a set without requirements).

Examples

head(rule_coverage("abundance"))

Description

Downloads the bundle of an apb-catalog release from GitHub into the user cache, so lookups use it without a package update. Later sessions keep using the newest bundle, shipped or downloaded. It works from the next apb-catalog release, the first to ship the bundle.

Usage

update_catalog(version = NULL)

Arguments

Value

The catalog_version() now in use, invisibly.

Examples

if (interactive()) {
  update_catalog()
}