SmallMoleculeEvidence

SmallMoleculeEvidence Class

Format

An R6Class generator object

Public fields

prefix

character [optional]

header_prefix

character [optional]

sme_id

integer

evidence_input_id

character

database_identifier

character

chemical_formula

character [optional]

smiles

character [optional]

inchi

character [optional]

chemical_name

character [optional]

uri

character [optional]

derivatized_form

Parameter [optional]

adduct_ion

character [optional]

exp_mass_to_charge

numeric

charge

integer

theoretical_mass_to_charge

numeric

spectra_ref

list( SpectraRef )

identification_method

Parameter

ms_level

Parameter

id_confidence_measure

list( numeric ) [optional]

rank

integer

opt

list( OptColumnMapping ) [optional]

comment

list( Comment ) [optional]

Methods

Public methods

• SmallMoleculeEvidence$new()

• SmallMoleculeEvidence$toJSON()

• SmallMoleculeEvidence$fromJSON()

• SmallMoleculeEvidence$toJSONString()

• SmallMoleculeEvidence$fromJSONString()

• SmallMoleculeEvidence$toDataFrame()

• SmallMoleculeEvidence$fromDataFrame()

• SmallMoleculeEvidence$clone()

---

Method new()

Create a new SmallMoleculeEvidence.

Usage

SmallMoleculeEvidence$new(
  sme_id,
  evidence_input_id,
  database_identifier,
  exp_mass_to_charge,
  charge,
  theoretical_mass_to_charge,
  spectra_ref,
  identification_method,
  ms_level,
  rank,
  prefix = "SME",
  header_prefix = "SEH",
  chemical_formula = NULL,
  smiles = NULL,
  inchi = NULL,
  chemical_name = NULL,
  uri = NULL,
  derivatized_form = NULL,
  adduct_ion = NULL,
  id_confidence_measure = NULL,
  opt = NULL,
  comment = NULL,
  ...
)

Arguments

sme_id

The small molecule evidence id.

evidence_input_id

The evidence input id.

database_identifier

The database identifier.

exp_mass_to_charge

The experimental mass to charge of the evidence.

charge

The charge of the evidence.

theoretical_mass_to_charge

The theoretical mass to charge.

spectra_ref

The references to source spectra list( SpectraRef ).

identification_method

The identification method Parameter.

ms_level

The ms level used for evidence Parameter.

rank

The database search / id rank.

prefix

'SMF'.

header_prefix

'SFH'.

chemical_formula

The chemical formula.

smiles

The SMILES string.

inchi

The INCHI identifier.

chemical_name

The chemical name.

uri

External URI.

derivatized_form

The derivatized form of the molecule.

adduct_ion

The adduct ion.

id_confidence_measure

The confidence measure used.

opt

Optional columns and values.

comment

Comments.

...

local optional variable arguments.

---

Method toJSON()

Serialize to list object suitable for jsonlite

Usage

SmallMoleculeEvidence$toJSON()

---

Method fromJSON()

Deserialize from jsonlite list object

Usage

SmallMoleculeEvidence$fromJSON(SmallMoleculeEvidenceJson)

Arguments

SmallMoleculeEvidenceJson

list object.

---

Method toJSONString()

Serialize to JSON string.

Usage

SmallMoleculeEvidence$toJSONString()

---

Method fromJSONString()

Deserialize from JSON string

Usage

SmallMoleculeEvidence$fromJSONString(SmallMoleculeEvidenceJson)

Arguments

SmallMoleculeEvidenceJson

SmallMoleculeEvidenceJson string

---

Method toDataFrame()

Serialize to data frame

Usage

SmallMoleculeEvidence$toDataFrame()

---

Method fromDataFrame()

Deserialize from evidence data frame

Usage

SmallMoleculeEvidence$fromDataFrame(EvidenceDataFrame)

Arguments

EvidenceDataFrame

Evidence data frame

---

Method clone()

The objects of this class are cloneable with this method.

Usage

SmallMoleculeEvidence$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.