pyms.eic
Class to model a subset of data from an Intensity Matrix.
Classes:
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Represents an extracted subset of the chromatographic data. |
Functions:
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Given an intensity matrix and a list of masses, construct a |
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class
ExtractedIntensityMatrix(time_list, mass_list, intensity_array)[source] Bases:
BaseIntensityMatrixRepresents an extracted subset of the chromatographic data.
- Parameters
- 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.
Returns binned mass at index.
get_ms_at_index(ix)Returns a mass spectrum for a given scan index.
Returns the spectral intensities for scan index.
Returns time at given index.
Iterate over column 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
ixin each scan to a new value.Attributes:
Constructs a Base Peak Chromatogram from the data.
Returns an
IonChromatogramobject representing this EIC.Returns a copy of the intensity array.
Returns a copy of the intensity array as a list of lists of floats.
Returns a copy of the intensity matrix.
Returns a list of the masses.
Returns the intensity matrix as a list of lists of floats.
Returns the maximum m/z value in the spectrum.
Returns the minimum m/z value in the spectrum.
Gets the size of intensity matrix.
Returns a copy of the time list.
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__eq__(other) Return whether this intensity matrix object is equal to another object.
- Parameters
other – The other object to test equality with.
- Return type
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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
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crop_mass(mass_min, mass_max) Crops mass spectrum.
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dump(file_name, protocol=3) Dumps an object to a file through
pickle.dump().
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property
eic Returns an
IonChromatogramobject representing this EIC.- Return type
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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
- Returns
Ion chromatogram at given index.
- Authors
Qiao Wang, Andrew Isaac, Vladimir Likic
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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.
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get_index_at_time(time) Returns the nearest index corresponding to the given time.
- Parameters
time (
float) – Time in seconds- Return type
- Returns
Nearest index corresponding to given time
- Authors
Lewis Lee, Tim Erwin, Vladimir Likic
Changed in version 2.3.0: Now returns
-1if no index is found.
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get_index_of_mass(mass) Returns the index of the nearest binned mass to the given mass.
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get_mass_at_index(ix) Returns binned mass at index.
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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
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get_scan_at_index(ix) Returns the spectral intensities for scan index.
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get_time_at_index(ix) Returns time at given index.
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property
intensity_array Returns a copy of the intensity array.
- Return type
- Returns
Matrix of intensity values.
- Authors
Andrew Isaac, Lewis Lee
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property
intensity_array_list Returns a copy of the intensity array as a list of lists of floats.
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property
intensity_matrix Returns a copy of the intensity matrix.
- Return type
- Returns
Matrix of intensity values.
- Author
Andrew Isaac
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property
mass_list Returns a list of the masses.
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property
matrix_list Returns the intensity matrix as a list of lists of floats.
- Return type
- Returns
Matrix of intensity values
- Author
Andrew Isaac
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property
max_mass Returns the maximum m/z value in the spectrum.
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property
min_mass Returns the minimum m/z value in the spectrum.
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null_mass(mass) Ignore given (closest) mass in spectra.
- Parameters
mass (
float) – Mass value to remove- Author
Andrew Isaac
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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. Default5.- Author
Vladimir Likic
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set_ic_at_index(ix, ic) Sets the intensity of the mass at index
ixin each scan to a new value.- Parameters
ix (
int) – Index of an ion chromatogram in the intensity data matrix to be setic (
IonChromatogram) – Ion chromatogram that will be copied at positionixin the data matrix
The length of the ion chromatogram must match the appropriate dimension of the intensity matrix.
- Author
Vladimir Likic
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property
size Gets the size of intensity matrix.
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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
ExtractedIntensityMatrixfor those masses.The masses can either be:
single masses (of type
float),an iterable of masses.
left_boundandright_boundspecify a range in which to include values for around each mass. For example, a mass of169with bounds of0.3and0.7would include every mass between168.7and169.7(inclusive on both sides).Set the bounds to
0to include only the given masses.- Parameters
- Return type