`pyms.eic`¶

Class to model a subset of data from an Intensity Matrix.

Classes:

ExtractedIntensityMatrix(time_list, ...)

Represents an extracted subset of the chromatographic data.

Functions:

build_extracted_intensity_matrix(im, masses)

Given an intensity matrix and a list of masses, construct a ExtractedIntensityMatrix for those masses.

class ExtractedIntensityMatrix(time_list, mass_list, intensity_array)[source]¶

Bases: BaseIntensityMatrix

Represents an extracted subset of the chromatographic data.

Parameters:

time_list (Sequence[float]) – Retention time values
mass_list (Sequence[float]) – Binned mass values
intensity_array (Union[Sequence[Sequence[float]], ndarray]) – List of lists of binned intensity values per scan

Authors:

Dominic Davis-Foster

New in version 2.3.0.

Methods:

`__eq__`(other)	Return whether this intensity matrix object is equal to another object.
`__len__`()	Returns the number of scans in the intensity matrix.
`crop_mass`(mass_min, mass_max)	Crops mass spectrum.
`dump`(file_name[, protocol])	Dumps an object to a file through `pickle.dump()`.
`get_ic_at_index`(ix)	Returns the ion chromatogram at the specified index.
`get_ic_at_mass`([mass])	Returns the ion chromatogram for the nearest binned mass to the specified mass.
`get_index_at_time`(time)	Returns the nearest index corresponding to the given time.
`get_index_of_mass`(mass)	Returns the index of the nearest binned mass to the given mass.
`get_mass_at_index`(ix)	Returns binned mass at index.
`get_ms_at_index`(ix)	Returns a mass spectrum for a given scan index.
`get_scan_at_index`(ix)	Returns the spectral intensities for scan index.
`get_time_at_index`(ix)	Returns time at given index.
`iter_ic_indices`()	Iterate over column indices.
`iter_ms_indices`()	Iterates over row indices.
`null_mass`(mass)	Ignore given (closest) mass in spectra.
`reduce_mass_spectra`([n_intensities])	Reduces the mass spectra by retaining the top n_intensities, discarding all other intensities.
`set_ic_at_index`(ix, ic)	Sets the intensity of the mass at index `ix` in each scan to a new value.

Attributes:

`bpc`	Constructs a Base Peak Chromatogram from the data.
`eic`	Returns an `IonChromatogram` object representing this EIC.
`intensity_array`	Returns a copy of the intensity array.
`intensity_array_list`	Returns a copy of the intensity array as a list of lists of floats.
`intensity_matrix`	Returns a copy of the intensity matrix.
`mass_list`	Returns a list of the masses.
`matrix_list`	Returns the intensity matrix as a list of lists of floats.
`max_mass`	Returns the maximum m/z value in the spectrum.
`min_mass`	Returns the minimum m/z value in the spectrum.
`size`	Gets the size of intensity matrix.
`time_list`	Returns a copy of the time list.

__eq__(other)¶

Return whether this intensity matrix object is equal to another object.

Parameters:: other – The other object to test equality with.
Return type:: bool

__len__()¶

Returns the number of scans in the intensity matrix.

Return type:: int

property bpc¶

Constructs a Base Peak Chromatogram from the data.

This represents the most intense ion – out of those used to create the ExtractedIntensityMatrix – for each scan.

Authors:: Dominic Davis-Foster

New in version 2.3.0.

Return type:: IonChromatogram

crop_mass(mass_min, mass_max)¶

Crops mass spectrum.

Parameters:

mass_min (float) – Minimum mass value
mass_max (float) – Maximum mass value

Author:

Andrew Isaac

dump(file_name, protocol=3)¶

Dumps an object to a file through pickle.dump().

Parameters:

file_name (Union[str, Path, PathLike]) – Filename to save the dump as.
protocol (int) – The pickle protocol to use. Default 3.

Authors:

Vladimir Likic, Dominic Davis-Foster (pathlib and pickle protocol support)

property eic¶

Returns an IonChromatogram object representing this EIC.

Return type:: ExtractedIonChromatogram

get_ic_at_index(ix)¶

Returns the ion chromatogram at the specified index.

Parameters:: ix (int) – Index of an ion chromatogram in the intensity data matrix.
Return type:: IonChromatogram
Returns:: Ion chromatogram at given index.
Authors:: Qiao Wang, Andrew Isaac, Vladimir Likic

get_ic_at_mass(mass=None)[source]¶

Returns the ion chromatogram for the nearest binned mass to the specified mass.

If no mass value is given, the function returns the extracted ion chromatogram.

Parameters:: mass (Optional[float]) – Mass value of an ion chromatogram. Default None.
Return type:: IonChromatogram
Returns:: Ion chromatogram for given mass
Authors:: Andrew Isaac, Vladimir Likic

get_index_at_time(time)¶

Returns the nearest index corresponding to the given time.

Parameters:: time (float) – Time in seconds
Return type:: int
Returns:: Nearest index corresponding to given time
Authors:: Lewis Lee, Tim Erwin, Vladimir Likic

Changed in version 2.3.0: Now returns -1 if no index is found.

get_index_of_mass(mass)¶

Returns the index of the nearest binned mass to the given mass.

Parameters:: mass (float) – Mass to lookup in list of masses
Author:: Andrew Isaac
Return type:: int

get_mass_at_index(ix)¶

Returns binned mass at index.

Parameters:: ix (int) – Index of binned mass
Return type:: float
Returns:: Binned mass
Author:: Andrew Isaac

get_ms_at_index(ix)¶

Returns a mass spectrum for a given scan index.

Parameters:: ix (int) – The index of the scan.
Author:: Andrew Isaac
Return type:: MassSpectrum

get_scan_at_index(ix)¶

Returns the spectral intensities for scan index.

Parameters:: ix (int) – The index of the scan
Return type:: List[float]
Returns:: Intensity values of scan spectra
Author:: Andrew Isaac

get_time_at_index(ix)¶

Returns time at given index.

Parameters:: ix (int)
Authors:: Lewis Lee, Vladimir Likic
Return type:: float

property intensity_array¶

Returns a copy of the intensity array.

Return type:: ndarray
Returns:: Matrix of intensity values.
Authors:: Andrew Isaac, Lewis Lee

property intensity_array_list¶

Returns a copy of the intensity array as a list of lists of floats.

Return type:: List[List[float]]
Returns:: Matrix of intensity values.
Author:: Andrew Isaac

property intensity_matrix¶

Returns a copy of the intensity matrix.

Return type:: ndarray
Returns:: Matrix of intensity values.
Author:: Andrew Isaac

iter_ic_indices()¶

Iterate over column indices.

Return type:: Iterator[int]

iter_ms_indices()¶

Iterates over row indices.

Return type:: Iterator[int]

property mass_list¶

Returns a list of the masses.

Authors:: Qiao Wang, Andrew Isaac, Vladimir Likic
Return type:: List[float]

property matrix_list¶

Returns the intensity matrix as a list of lists of floats.

Return type:: ndarray
Returns:: Matrix of intensity values
Author:: Andrew Isaac

property max_mass¶

Returns the maximum m/z value in the spectrum.

Author:: Andrew Isaac
Return type:: Optional[float]

property min_mass¶

Returns the minimum m/z value in the spectrum.

Author:: Andrew Isaac
Return type:: Optional[float]

null_mass(mass)¶

Ignore given (closest) mass in spectra.

Parameters:: mass (float) – Mass value to remove
Author:: Andrew Isaac

reduce_mass_spectra(n_intensities=5)¶

Reduces the mass spectra by retaining the top n_intensities, discarding all other intensities.

Parameters:: n_intensities (int) – The number of top intensities to keep. Default 5.
Author:: Vladimir Likic

set_ic_at_index(ix, ic)¶

Sets the intensity of the mass at index ix in each scan to a new value.

Parameters:

ix (int) – Index of an ion chromatogram in the intensity data matrix to be set
ic (IonChromatogram) – Ion chromatogram that will be copied at position ix in the data matrix

The length of the ion chromatogram must match the appropriate dimension of the intensity matrix.

Author:: Vladimir Likic

property size¶

Gets the size of intensity matrix.

Return type:: Tuple[int, int]
Returns:: Number of rows and cols
Authors:: Qiao Wang, Andrew Isaac, Luke Hodkinson, Vladimir Likic

property time_list¶

Returns a copy of the time list.

Return type:: List[float]
Returns:: List of retention times
Authors:: Andrew Isaac, Lewis Lee, Vladimir Likic

build_extracted_intensity_matrix(im, masses, left_bound=0.5, right_bound=0.5)[source]¶

Given an intensity matrix and a list of masses, construct a ExtractedIntensityMatrix for those masses.

The masses can either be:

single masses (of type float),
an iterable of masses.

left_bound and right_bound specify a range in which to include values for around each mass. For example, a mass of 169 with bounds of 0.3 and 0.7 would include every mass between 168.7 and 169.7 (inclusive on both sides).

Set the bounds to 0 to include only the given masses.

Parameters:

im (IntensityMatrix)
masses (Sequence[Union[float, Iterable[float]]])
left_bound (float) – Default 0.5.
right_bound (float) – Default 0.5.

Return type:

ExtractedIntensityMatrix

pyms.eic¶

`pyms.eic`¶