MsRun: MsRun

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

MsRun

Description

MsRun Class

Format

An R6Class generator object

Public fields

id

integer

name

character

location

character

instrument_ref

Instrument [optional]

format

Parameter [optional]

id_format

Parameter [optional]

fragmentation_method

list( Parameter ) [optional]

scan_polarity

list( Parameter ) [optional]

hash

character [optional]

hash_method

Parameter [optional]

Methods

Public methods

• MsRun$new()

• MsRun$toJSON()

• MsRun$fromJSON()

• MsRun$toJSONString()

• MsRun$fromJSONString()

• MsRun$toDataFrame()

• MsRun$fromDataFrame()

• MsRun$clone()

---

Method new()

Create an MsRun

Usage

MsRun$new(
  id,
  name,
  location,
  instrument_ref = NULL,
  format = NULL,
  id_format = NULL,
  fragmentation_method = NULL,
  scan_polarity = NULL,
  hash = NULL,
  hash_method = NULL,
  ...
)

Arguments

id

MsRun id.

name

MsRun name.

location

the location URI to retrieve the MsRun file.

instrument_ref

Link to the Instrument used to acquire this MsRun.

format

CV parameter defining the file format Parameter.

id_format

CV parameter defining the mass spec id format Parameter.

fragmentation_method

Fragementation methods list( Parameter ).

scan_polarity

Scan polarities present in the file list( Parameter ).

hash

Hash value of the file using the hash_method.

hash_method

Parameter

...

local optional variable arguments

---

Method toJSON()

Serialize to list object suitable for jsonlite

Usage

MsRun$toJSON()

---

Method fromJSON()

Deserialize from jsonlite list object

Usage

MsRun$fromJSON(MsRunJson)

Arguments

MsRunJson

list object.

---

Method toJSONString()

Serialize to JSON string.

Usage

MsRun$toJSONString()

---

Method fromJSONString()

Deserialize from JSON string

Usage

MsRun$fromJSONString(MsRunJson)

Arguments

MsRunJson

JSON string

---

Method toDataFrame()

Serialize to data frame

Usage

MsRun$toDataFrame()

---

Method fromDataFrame()

Deserialize from ms run data frame

Usage

MsRun$fromDataFrame(MsRunDataFrame)

Arguments

MsRunDataFrame

MsRun data frame

---

Method clone()

The objects of this class are cloneable with this method.

Usage

MsRun$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.