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 catalog 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 "intensity_norm_settings", 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. enforce checks the set's requirements against the rule's levels once, when the catalog opens.

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 set to the rule levels of one software version.

Usage

Catalog$new(software, software_version, set_name, enforce = NULL)

Arguments

Catalog$fields()

Every cataloged field the rule declares, one row per field, as catalog_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$new("DIA-NN", "2.2.0", "abundance_alpha")
catalog$levels$peptidoform_ion$layers[["intensity"]]
catalog$levels$peptidoform_ion$layers$keys()

Description

The whole catalog, every set of the bundle, or one set: one row per entry and software version it applies to, as ⁠apb-catalog table⁠ prints it.

Usage

catalog_table(set_name = NULL)

Arguments

Value

A data frame with columns set, source (who writes the field: the quantification software, an app or ⁠annotation:<convention>⁠), version (the version label; * for an app's or an annotation's entry, which applies to every version), software_version_pattern (NA for an entry of every software version), level, slot (layers, var, obs or varm), table (the varm table, else NA), name (the field's 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(catalog_table("confidence_alpha"))

Description

Reports the bundle lookups answer from: its version, whether it was shipped with the package or installed 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

obs[c("group")] holds every column the key names, each under its own name, where obs[["group"]] signals UnresolvedField because there are several.

Value

The class generator, not exported: a Level's var and obs are its objects.

Super class

Slot -> Columns

Methods

Public methods

• Columns$new()

• Columns$get_all()

• Columns$clone()

Columns$new()

Bind one var or obs slot of a level.

Usage

Columns$new(level, location, lookup, read, named, combine)

Arguments

Columns$get_all()

Every field the names name, in order; an error for a name that is neither a key nor the level's own.

Usage

Columns$get_all(names)

Arguments

Returns

A data frame; names without data.

Columns$clone()

The objects of this class are cloneable with this method.

Usage

Columns$clone(deep = FALSE)

Arguments

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.

Composes the named sets alone: apb_alpha, the fields apb2 convert writes, answers only when named. A key routes to the sets that define it; two sets naming different fields for one key on one level is an error. With no set named, every name is the level's own. A named set that can answer nothing on the result, because its app has not run or the result records no sample annotation, is an error saying what to run. enforce checks the requirements once, here.

DataCatalog$answering_sets(result) returns the sets DataCatalog$new(result, name) opens, as a character vector: every set but one whose app has not run on the result or whose annotation it does not record. It signals no error for such a set, so a consumer can leave it out.

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 the named sets, and no others, to the levels of one result.

Usage

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

Arguments

DataCatalog$fields()

Every cataloged field of the result in every composed set, one row per field, as catalog_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$new(result, "confidence_alpha")
dim(catalog$levels$peptidoform_ion$layers[["pep"]])
catalog$levels$peptidoform_ion$layers$name("pep")

Description

anndataR's slots of one level: X, layers, var, obs, obs_names and var_names. X is the level's primary layer and layers its other layers, observations by variables; a key may name the primary layer, and then answers X. cat$levels$protein$layers[["intensity"]] looks the name up as one of the catalog's keys first, then as the level's own name in that slot, and signals an error when it is neither; a prefix makes the lookup exact, "c:q_value" the confidence set alone, "v:q_value" the level's own name alone. obs[c("group", "Run")] reads every column the names name as a data frame.

Value

The class generator, not exported: a DataCatalog's levels hold its objects, which the catalog creates.

Public fields

Active bindings

Methods

Public methods

• Level$new()

• Level$clone()

Level$new()

Bind one level to the catalog's lookups.

Usage

Level$new(name, level, lookup)

Arguments

Level$clone()

The objects of this class are cloneable with this method.

Usage

Level$clone(deep = FALSE)

Arguments

Description

The slots of a Level without data: layers, var and obs answer a key with the field's name, a varm column as table/column. There is no X, obs_names, var_names or own name: a name that is no key the level answers signals an error.

Value

The class generator, not exported: a Catalog's levels hold its objects, which the catalog creates.

Public fields

Methods

Public methods

• LevelNames$new()

• LevelNames$clone()

LevelNames$new()

Bind one rule level to the catalog's lookups.

Usage

LevelNames$new(name, lookup)

Arguments

LevelNames$clone()

The objects of this class are cloneable with this method.

Usage

LevelNames$clone(deep = FALSE)

Arguments

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 the rhdf5 package, with which anndataR reads it.

Usage

read_parsed_levels(path)

Arguments

Value

A ParsedLevels object.

Input layout

apb2's convert command writes the result; each format records its format name and version, and a result of another format or version is refused:

• Parquet: a directory ending in .parquet whose manifest.json (format apb2-parsed-levels-parquet, version 9) names every level and table. Each level is a folder under ⁠levels/⁠ with obs.parquet, var.parquet, one file per layer in ⁠layers/⁠ (features by observations) and the tables of ⁠obsm/⁠, ⁠varm/⁠, ⁠obsp/⁠ and ⁠varp/⁠. The result's own tables are in ⁠annotation_tables/⁠ and ⁠feature_relations/⁠.

• DuckDB: one .duckdb file (format apb2-parsed-levels-duckdb, version 8) holding the same manifest in the table apb2_result_metadata; each table the manifest names is a database table.

• h5ad: one .h5ad file of a one-level result in anndata's layout (format apb2-parsed-levels, version 8), with apb2's storage descriptor in uns$apb. An .h5ad file other software wrote has none and is refused.

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 cataloged or required field of each rule level the set reviews; a set without vendor entries 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 required field is unsupported, warn when a recommended one is, pass otherwise; an unsupported optional field is listed but passes.

Usage

rule_coverage(set_name)

Arguments

Value

A data frame with columns software (the quantification software of the rule), version (the label), software_version_pattern, level, slot, table (the varm table, else NA), name (the field's name, NA when unsupported), key, kind, one ⁠qualifier.<name>⁠ column per other qualifier of the set, as in catalog_table(), producer (the app, NA for the quantification software's fields), requirement, needs (what to run before the field exists) and verdict (NA for a set without requirements).

Examples

head(rule_coverage("abundance_alpha"))

Description

Every set of the bundle with its prefix, its purpose, its users and its number of entries. The prefix asks the set alone, as "c:q_value".

Usage

sets()

Value

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

Examples

sets()

Description

[[ reads a key, else the level's own name; ⁠$keys()⁠ lists the catalog's keys only. ⁠$get()⁠ returns NULL where [[ signals an error, ⁠$name()⁠ the field's name; both take the qualifiers a key leaves open. A set's prefix, "c:q_value", asks that set alone and never the level's own name; "v:q_value" asks the level's own name alone. The design follows the Python package cf_xarray, whose accessor finds a variable by its CF-convention standard name before its own name.

Value

The class generator, not exported: a Level's layers is its object.

Methods

Public methods

• Slot$new()

• Slot$get()

• Slot$name()

• Slot$keys()

• Slot$clone()

Slot$new()

Bind one slot of a level.

Usage

Slot$new(level, location, lookup, read, named)

Arguments

Slot$get()

The field a key names, narrowed by further qualifiers, else the level's own field of that name.

Usage

Slot$get(key, ...)

Arguments

Returns

A matrix for layers, a vector for var and obs, a name without data; NULL when it is neither.

Slot$name()

The name of the field get reads; an error when the name is neither a key the level answers nor one of its own names.

Usage

Slot$name(key, ...)

Arguments

Returns

The field's name, such as "PEP"; table/column for a column of a varm table.

Slot$keys()

The keys the level offers in this slot.

Usage

Slot$keys()

Returns

A character vector.

Slot$clone()

The objects of this class are cloneable with this method.

Usage

Slot$clone(deep = FALSE)

Arguments

Description

Installs a bundle archive into the user cache, so lookups use it without a package update. apb-catalog's ⁠make bundle⁠ writes the archive, as build/apb-catalog-bundle.tar.gz. Later sessions keep using the newest bundle, shipped or installed. Nothing is downloaded.

Usage

update_catalog(path)

Arguments

Value

The catalog_version() now in use, invisibly.

Examples

if (interactive()) {
    update_catalog("apb-catalog/build/apb-catalog-bundle.tar.gz")
}