SmallMoleculeSummary: SmallMoleculeSummary

In lifs-tools/rmzTab-m: R Package Client for mzTab-M Reference Implementation and Validation API

SmallMoleculeSummary

Description

SmallMoleculeSummary Class

Format

An R6Class generator object

Public fields

prefix

character [optional]

header_prefix

character [optional]

sml_id

integer

smf_id_refs

list( integer ) [optional]

database_identifier

list( character ) [optional]

chemical_formula

list( character ) [optional]

smiles

list( character ) [optional]

inchi

list( character ) [optional]

chemical_name

list( character ) [optional]

uri

list( character ) [optional]

theoretical_neutral_mass

list( numeric ) [optional]

adduct_ions

list( character ) [optional]

reliability

character [optional]

best_id_confidence_measure

Parameter [optional]

best_id_confidence_value

numeric [optional]

abundance_assay

list( numeric ) [optional]

abundance_study_variable

list( numeric ) [optional]

abundance_variation_study_variable

list( numeric ) [optional]

opt

list( OptColumnMapping ) [optional]

comment

list( Comment ) [optional]

Methods

Public methods

• SmallMoleculeSummary$new()

• SmallMoleculeSummary$toJSON()

• SmallMoleculeSummary$fromJSON()

• SmallMoleculeSummary$toJSONString()

• SmallMoleculeSummary$fromJSONString()

• SmallMoleculeSummary$toDataFrame()

• SmallMoleculeSummary$fromDataFrame()

• SmallMoleculeSummary$clone()

---

Method new()

Create a new SmallMoleculeSummary.

Usage

SmallMoleculeSummary$new(
  sml_id,
  prefix = "SML",
  header_prefix = "SMH",
  smf_id_refs = NULL,
  database_identifier = NULL,
  chemical_formula = NULL,
  smiles = NULL,
  inchi = NULL,
  chemical_name = NULL,
  uri = NULL,
  theoretical_neutral_mass = NULL,
  adduct_ions = NULL,
  reliability = NULL,
  best_id_confidence_measure = NULL,
  best_id_confidence_value = NULL,
  abundance_assay = NULL,
  abundance_study_variable = NULL,
  abundance_variation_study_variable = NULL,
  opt = NULL,
  comment = NULL,
  ...
)

Arguments

sml_id

The small molecule summary id.

prefix

'SML'.

header_prefix

'SMH'.

smf_id_refs

References by id to SmallMoleculeFeatures.

database_identifier

The database identifiers.

chemical_formula

The chemical formulas.

smiles

The SMILES strings.

inchi

The INCHI identifiers.

chemical_name

The chemical names.

uri

External URIs.

theoretical_neutral_mass

The theoretical neutral masses.

adduct_ions

The adduct ions.

reliability

The reliability according to the system defined in the Metadata section.

best_id_confidence_measure

The best id confidence measure Parameter.

best_id_confidence_value

The best id confidence value.

abundance_assay

The abundances over all assays.

abundance_study_variable

The abundances over study variables.

abundance_variation_study_variable

The abundances variation over study variables.

opt

Optional columns and values.

comment

Comments.

...

local optional variable arguments.

---

Method toJSON()

Serialize to list object suitable for jsonlite

Usage

SmallMoleculeSummary$toJSON()

---

Method fromJSON()

Deserialize from jsonlite list object

Usage

SmallMoleculeSummary$fromJSON(SmallMoleculeSummaryJson)

Arguments

SmallMoleculeSummaryJson

list object.

---

Method toJSONString()

Serialize to JSON string.

Usage

SmallMoleculeSummary$toJSONString()

---

Method fromJSONString()

Deserialize from JSON string

Usage

SmallMoleculeSummary$fromJSONString(SmallMoleculeSummaryJson)

Arguments

SmallMoleculeSummaryJson

SmallMoleculeSummaryJson string

---

Method toDataFrame()

Serialize to data frame

Usage

SmallMoleculeSummary$toDataFrame()

---

Method fromDataFrame()

Deserialize from summary data frame

Usage

SmallMoleculeSummary$fromDataFrame(SummaryDataFrame)

Arguments

SummaryDataFrame

Summary data frame

---

Method clone()

The objects of this class are cloneable with this method.

Usage

SmallMoleculeSummary$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

lifs-tools/rmzTab-m documentation built on Jan. 26, 2023, 4:45 p.m.