Class Chromatogram

Hierarchy

Chromatogram

Constructors

constructor

new Chromatogram(times: number[], series: {}): Chromatogram

- Defined in chromatography.d.ts:349
Parameters
- times: number[]
  
  Array of time points.
- series: {}
  
  Dictionary of series.
  - [key: string]: ChromatogramSeriesData
Returns Chromatogram

Accessors

firstTime

get firstTime(): number

- Defined in chromatography.d.ts:420
Returns the first time value.

Returns number

lastTime

get lastTime(): number

- Defined in chromatography.d.ts:425
Returns the last time value.

Returns number

length

get length(): number

- Defined in chromatography.d.ts:357
Returns the number of time points.

Returns number

Methods

addSeries

addSeries(seriesName: string, data: ChromatogramSeriesData, options?: AddSeriesOptions): Chromatogram

- Defined in chromatography.d.ts:399
Add a new series.

Parameters
- seriesName: string
  
  Name of the series to add.
- data: ChromatogramSeriesData
  
  Series data.
- Optional options: AddSeriesOptions
Returns Chromatogram

applyLockMass

applyLockMass(mfs: string | string[], options?: ApplyLockMassOptions): LockMassReferenceUsed

- Defined in chromatography.d.ts:562
Recalculates series for GC/MS with lock mass.

Parameters
- mfs: string | string[]
  
  Reference molecular formula(s).
- Optional options: ApplyLockMassOptions
Returns LockMassReferenceUsed

calculateBpc

calculateBpc(options?: CalculateOptions): Chromatogram

- Defined in chromatography.d.ts:476
Calculate the base peak chromatogram (BPC) and save it in the "bpc" series.

Parameters
- Optional options: CalculateOptions
Returns Chromatogram

calculateEic

calculateEic(targetMass: number | number[], options?: CalculateForMassOptions): ChromatogramSeries1D

- Defined in chromatography.d.ts:484
Calculate the extracted ion chromatogram (EIC) and save it in a new series.

Parameters
- targetMass: number | number[]
  
  Mass or masses for which to extract the spectrum.
- Optional options: CalculateForMassOptions
Returns ChromatogramSeries1D
- The created series.

calculateForMF

calculateForMF(targetMF: string, options?: CalculateForMFOptions): ChromatogramSeries1D

- Defined in chromatography.d.ts:495
Calculate mass spectrum by filtering for a molecular formula.

Parameters
- targetMF: string
  
  MF for which to extract the spectrum.
- Optional options: CalculateForMFOptions
Returns ChromatogramSeries1D
- The created series.

calculateLength

calculateLength(seriesName: string, options?: CalculateOptions): Chromatogram

- Defined in chromatography.d.ts:470
Calculate length (number of points of each related information) and save it in the "length" series.

Parameters
- seriesName: string
  
  Name of the series to make calculation on. It must be a 2D series.
- Optional options: CalculateOptions
Returns Chromatogram

calculateTic

calculateTic(options?: CalculateOptions): Chromatogram

- Defined in chromatography.d.ts:463
Calculate the "tic" series from the "ms" one.

Parameters
- Optional options: CalculateOptions
Returns Chromatogram

copy

copy(): Chromatogram

- Defined in chromatography.d.ts:535
Returns a copy of the chromatogram.

Returns Chromatogram

deconvolution

deconvolution(options?: DeconvolutionOptions): DeconvolutionResult

- Defined in chromatography.d.ts:579
Performing non-negative matrix factorization solving argmin_(A >= 0, S >= 0) 1 / 2 * ||Y - AS||_2^2 + lambda * ||S||_1

Parameters
- Optional options: DeconvolutionOptions
Returns DeconvolutionResult

deleteSeries

deleteSeries(seriesName: string): Chromatogram

- Defined in chromatography.d.ts:392
Delete a series.

Parameters
- seriesName: string
Returns Chromatogram

filter

filter(callback: (index: number, time: number) => boolean, options?: FilterOptions): Chromatogram

- Defined in chromatography.d.ts:448
Will filter the entries based on the index and time.

Parameters
- callback: (index: number, time: number) => boolean
  - - (index: number, time: number): boolean
    - Parameters
      - index: number
      - time: number
      Returns boolean
- Optional options: FilterOptions
Returns Chromatogram

getClosestData

getClosestData<DataType>(time: number, options?: GetClosestDataOptions): GetClosestDataResult<DataType>

- Defined in chromatography.d.ts:527
Returns the closest mass spectrum to a specific retention time

Type parameters
- DataType = number[]
Parameters
- time: number
  
  Retention time
- Optional options: GetClosestDataOptions
Returns GetClosestDataResult<DataType>

getClosestTime

getClosestTime(time: number): number

- Defined in chromatography.d.ts:521
Returns the index of the closest real time to the specified one.

Parameters
- time: number
  
  Retention time.
Returns number
- Time index.

getMzVsTimesMatrix

getMzVsTimesMatrix(range: ChromatogramRange): any

- Defined in chromatography.d.ts:586
Return the submatrix, times, and mass x axis for each range

Parameters
- range: ChromatogramRange
Returns any

getPeaks

getPeaks(options?: GetPeaksOptions): ChromatogramPeak[]

- Defined in chromatography.d.ts:458
Apply the GSD peak picking algorithm.

Parameters
- Optional options: GetPeaksOptions
Returns ChromatogramPeak[]
- List of GSD objects

getSeries

getSeries(seriesName: string): ChromatogramSeries<number[] | number[][][]>

- Defined in chromatography.d.ts:363
Find the series from its name.

Parameters
- seriesName: string
  
  Name of the series.
Returns ChromatogramSeries<number[] | number[][][]>

getSeries1D

getSeries1D(seriesName: string): ChromatogramSeries1D

- Defined in chromatography.d.ts:370
Find the series from its name. Throws an error if it is not a 1D series.

Parameters
- seriesName: string
Returns ChromatogramSeries1D

getSeries2D

getSeries2D(seriesName: string): ChromatogramSeries2D

- Defined in chromatography.d.ts:377
Find the series from its name. Throws an error if it is not a 2D series.

Parameters
- seriesName: string
Returns ChromatogramSeries2D

getSeriesNames

getSeriesNames(): string[]

- Defined in chromatography.d.ts:382
Returns the names of all series.

Returns string[]

getTimes

getTimes(): number[]

- Defined in chromatography.d.ts:430
Returns the time values.

Returns number[]

hasMass

hasMass(): boolean

- Defined in chromatography.d.ts:387
Returns whether the chromatogram has an "ms" series.

Returns boolean

hasSeries

hasSeries(seriesName: string): boolean

- Defined in chromatography.d.ts:409
Returns whether the series exists.

Parameters
- seriesName: string
  
  Name of the series to check.
Returns boolean

integrate

integrate(ranges: ChromatogramRange[], options?: IntegrateOptions): IntegrateResult[]

- Defined in chromatography.d.ts:505
Returns an array containing the integral of various ranges

Parameters
- ranges: ChromatogramRange[]
- Optional options: IntegrateOptions
Returns IntegrateResult[]

meanFilter

meanFilter(seriesName: string, options?: MeanFilterOptions): ChromatogramSeries2D

- Defined in chromatography.d.ts:542
Filter the given 2D series based on it's median value.

Parameters
- seriesName: string
  
  Name of the series to filter.
- Optional options: MeanFilterOptions
Returns ChromatogramSeries2D

merge

merge(options?: MergeOptions): MergeResult

- Defined in chromatography.d.ts:514
Returns a mass spectrum corresponding to the merge of a range.

Parameters
- Optional options: MergeOptions
Returns MergeResult

percentageFilter

percentageFilter(seriesName: string, options?: PercentageFilterOptions): ChromatogramSeries2D

- Defined in chromatography.d.ts:552
Filter the given 2D series based on the percentage of the highest value

Parameters
- seriesName: string
  
  Name of the series to filter.
- Optional options: PercentageFilterOptions
Returns ChromatogramSeries2D

requiresSeries

requiresSeries(seriesName: string): void

- Defined in chromatography.d.ts:415
Throws an error if the series does not exist.

Parameters
- seriesName: string
  
  Name of the series to check.
Returns void

rescaleTime

rescaleTime(conversionFunction: (time: number) => number): Chromatogram

- Defined in chromatography.d.ts:442
Modifies the time applying the conversion function.

Parameters
- conversionFunction: (time: number) => number
  - - (time: number): number
    - Parameters
      - time: number
      Returns number
Returns Chromatogram

setTimes

setTimes(times: number[]): Chromatogram

- Defined in chromatography.d.ts:436
Assign the time values.

Parameters
- times: number[]
  
  New time values.
Returns Chromatogram

toJSON

toJSON(): { series: {}; times: number[] }

- Defined in chromatography.d.ts:570
Returns a serializable representation of the chromatogram.

Returns { series: {}; times: number[] }
- series: {}
  - [key: string]: { data: ChromatogramSeriesData; meta?: object }
    - data: ChromatogramSeriesData
    - Optional meta?: object
- times: number[]