SmallMoleculeFeature: SmallMoleculeFeature

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

SmallMoleculeFeature

Description

SmallMoleculeFeature Class

Format

An R6Class generator object

Public fields

prefix

character [optional]

header_prefix

character [optional]

smf_id

integer

sme_id_refs

list( integer ) [optional]

sme_id_ref_ambiguity_code

integer [optional]

adduct_ion

character [optional]

isotopomer

Parameter [optional]

exp_mass_to_charge

numeric

charge

integer

retention_time_in_seconds

numeric [optional]

retention_time_in_seconds_start

numeric [optional]

retention_time_in_seconds_end

numeric [optional]

abundance_assay

list( numeric ) [optional]

opt

list( OptColumnMapping ) [optional]

comment

list( Comment ) [optional]

Methods

Public methods

• SmallMoleculeFeature$new()

• SmallMoleculeFeature$toJSON()

• SmallMoleculeFeature$fromJSON()

• SmallMoleculeFeature$toJSONString()

• SmallMoleculeFeature$fromJSONString()

• SmallMoleculeFeature$toDataFrame()

• SmallMoleculeFeature$fromDataFrame()

• SmallMoleculeFeature$clone()

---

Method new()

Create a new SmallMoleculeFeature.

Usage

SmallMoleculeFeature$new(
  smf_id,
  exp_mass_to_charge,
  charge,
  prefix = "SMF",
  header_prefix = "SFH",
  sme_id_refs = NULL,
  sme_id_ref_ambiguity_code = NULL,
  adduct_ion = NULL,
  isotopomer = NULL,
  retention_time_in_seconds = NULL,
  retention_time_in_seconds_start = NULL,
  retention_time_in_seconds_end = NULL,
  abundance_assay = NULL,
  opt = NULL,
  comment = NULL,
  ...
)

Arguments

smf_id

The small molecule feature id.

exp_mass_to_charge

The experimental mass to charge of the feature.

charge

The charge of the feature.

prefix

'SMF'.

header_prefix

'SFH'.

sme_id_refs

References by id to SmallMoleculeEvidences.

sme_id_ref_ambiguity_code

Ambiguity code for SME id refs.

adduct_ion

The adduct ion.

isotopomer

The isotopomer.

retention_time_in_seconds

The feature's retention time in seconds.

retention_time_in_seconds_start

The feature's retention time start in seconds.

retention_time_in_seconds_end

The feature's retention time end in seconds.

abundance_assay

The abundances over all assays.

opt

Optional columns and values.

comment

Comments.

...

local optional variable arguments.

---

Method toJSON()

Serialize to list object suitable for jsonlite

Usage

SmallMoleculeFeature$toJSON()

---

Method fromJSON()

Deserialize from jsonlite list object

Usage

SmallMoleculeFeature$fromJSON(SmallMoleculeFeatureJson)

Arguments

SmallMoleculeFeatureJson

list object.

---

Method toJSONString()

Serialize to JSON string.

Usage

SmallMoleculeFeature$toJSONString()

---

Method fromJSONString()

Deserialize from JSON string

Usage

SmallMoleculeFeature$fromJSONString(SmallMoleculeFeatureJson)

Arguments

SmallMoleculeFeatureJson

SmallMoleculeFeatureJson string

---

Method toDataFrame()

Serialize to data frame

Usage

SmallMoleculeFeature$toDataFrame()

---

Method fromDataFrame()

Deserialize from feature data frame

Usage

SmallMoleculeFeature$fromDataFrame(FeatureDataFrame)

Arguments

FeatureDataFrame

Feature data frame

---

Method clone()

The objects of this class are cloneable with this method.

Usage

SmallMoleculeFeature$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.