Class Chromatogram

constructor

• new Chromatogram(
      times: DoubleArray,
      series?: Record<string, ChromatogramSeriesData>,
      options?: ChromatogramInitOptions,
  ): Chromatogram

  Construct a new chromatogram.

  Parameters

  • times: DoubleArray

    Array of time points.

  • Optionalseries: Record<string, ChromatogramSeriesData>

    Dictionary of series.

  • options: ChromatogramInitOptions = {}

  Returns Chromatogram

meta

series

times

firstTime

• get firstTime(): number

  Returns the first time value.

  Returns number

lastTime

• get lastTime(): number

  Returns the last time value.

  Returns number

length

• get length(): number

  Returns the number of time points.

  Returns number

addSeries

• addSeries(
      seriesName: string,
      data: DoubleArray | ChromatogramSeries2DData,
      options?: AddSeriesOptions,
  ): this

  Add a new series.

  Parameters

  • seriesName: string

    Name of the series to add.

  • data: DoubleArray | ChromatogramSeries2DData

    Series data.

  • options: AddSeriesOptions = {}

  Returns this

applyLockMass

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

  Recalculates series for GC/MS with lock mass.

  Parameters

  • mfs: string | string[]

    Reference molecular formula(s).

  • Optionaloptions: ApplyLockMassOptions

  Returns LockMassReferenceUsed

calculateBpc

• calculateBpc(options?: CalculateOptions): this

  Calculate the base peak chromatogram (BPC) and save it in the "bpc" series.

  Parameters

  • options: CalculateOptions = {}

  Returns this

calculateEic

• calculateEic(
      targetMass: string | number | number[],
      options?: CalculateEicOptions,
  ): ChromatogramSeries1D

  Calculate the extracted ion chromatogram (EIC) and save it in a new series.

  Parameters

  • targetMass: string | number | number[]

    Mass or masses for which to extract the spectrum.

  • options: CalculateEicOptions = {}

  Returns ChromatogramSeries1D

  • The created series.

calculateForMF

• calculateForMF(
      targetMF: string,
      options?: CalculateForMFOptions,
  ): Promise<ChromatogramSeries1D>

  Calculate mass spectrum by filtering for a molecular formula.

  Parameters

  • targetMF: string

    MF for which to extract the spectrum.

  • options: CalculateForMFOptions = {}

  Returns Promise<ChromatogramSeries1D>

  • The created series.

calculateLength

• calculateLength(seriesName: string, options?: CalculateOptions): this

  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.

  • options: CalculateOptions = {}

  Returns this

calculateTic

• calculateTic(options?: CalculateOptions): this

  Calculate the "tic" series from the "ms" one.

  Parameters

  • options: CalculateOptions = {}

  Returns this

copy

• copy(): Chromatogram

  Returns a copy of the chromatogram.

  Returns Chromatogram

deconvolution

• deconvolution(options: DeconvolutionOptions): DeconvolutionResult

  Performing non-negative matrix factorization solving argmin_(A >= 0, S >= 0) 1 / 2 * ||Y - AS||_2^2 + lambda * ||S||_1

  Parameters

  • options: DeconvolutionOptions

  Returns DeconvolutionResult

deleteSeries

• deleteSeries(seriesName: string): this

  Delete a series.

  Parameters

  • seriesName: string

  Returns this

filter

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

  Will filter the entries based on the index and time.

  Parameters

  • callback: (index: number, time: number) => boolean
  • Optionaloptions: FilterOptions

  Returns Chromatogram

getClosestData

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

  Returns the closest mass spectrum to a specific retention time

  Type Parameters

  • DataType extends ChromatogramSeriesData

  Parameters

  • time: number

    Retention time

  • Optionaloptions: GetClosestDataOptions

  Returns GetClosestDataResult<DataType>

getClosestTime

• getClosestTime(time: number): number

  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): MzVsTimesMatrixResult

  Return the submatrix, times, and mass x axis for each range

  Parameters

  • range: ChromatogramRange

  Returns MzVsTimesMatrixResult

getPeaks

• getPeaks(options?: GetPeaksOptions): ChromatogramPeak[]

  Apply the GSD peak picking algorithm.

  Parameters

  • Optionaloptions: GetPeaksOptions

  Returns ChromatogramPeak[]

  • List of GSD objects

getSeries

• getSeries(seriesName: string): ChromatogramSeries

  Find the series from its name.

  Parameters

  • seriesName: string

    Name of the series.

  Returns ChromatogramSeries

getSeries1D

• getSeries1D(seriesName: string): ChromatogramSeries1D

  Find the series from its name. Throws an error if it is not a 1D series.

  Parameters

  • seriesName: string

    Name of the series.

  Returns ChromatogramSeries1D

getSeries2D

• getSeries2D(seriesName: string): ChromatogramSeries2D

  Find the series from its name. Throws an error if it is not a 2D series.

  Parameters

  • seriesName: string

    Name of the series.

  Returns ChromatogramSeries2D

getSeriesNames

• getSeriesNames(): string[]

  Returns the names of all series.

  Returns string[]

getTimes

• getTimes(): DoubleArray

  Returns the time values.

  Returns DoubleArray

hasMass

• hasMass(): boolean

  Returns whether the chromatogram has an "ms" series.

  Returns boolean

hasSeries

• hasSeries(seriesName: string): boolean

  Returns whether the series exists.

  Parameters

  • seriesName: string

    Name of the series to check.

  Returns boolean

integrate

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

  Returns an array containing the integral of various ranges

  Parameters

  • ranges: ChromatogramRange[]
  • Optionaloptions: IntegrateOptions

  Returns IntegrateResult[]

meanFilter

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

  Filter the given 2D series based on its median value.

  Parameters

  • seriesName: string

    Name of the series to filter.

  • options: MeanFilterOptions = {}

  Returns ChromatogramSeries2D

merge

• merge(options?: MergeOptions): MergeResult

  Returns a mass spectrum corresponding to the merge of a range.

  Parameters

  • Optionaloptions: MergeOptions

  Returns MergeResult

percentageFilter

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

  Filter the given 2D series based on the percentage of the highest value

  Parameters

  • seriesName: string

    Name of the series to filter.

  • options: PercentageFilterOptions = {}

  Returns ChromatogramSeries2D

requiresSeries

• requiresSeries(seriesName: string): void

  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): this

  Modifies the time applying the conversion function.

  Parameters

  • conversionFunction: (time: number) => number

  Returns this

setTimes

• setTimes(times: DoubleArray): this

  Assign the time values.

  Parameters

  • times: DoubleArray

    New time values.

  Returns this

toJSON

• toJSON(): {
      series: {
          [k: string]: {
              data: DoubleArray
              | ChromatogramSeries2DData;
              meta: Record<string, unknown>;
          };
      };
      times: number[];
  }

  Returns a serializable representation of the chromatogram.

  Returns {
      series: {
          [k: string]: {
              data: DoubleArray | ChromatogramSeries2DData;
              meta: Record<string, unknown>;
          };
      };
      times: number[];
  }