Implementation of the IDemultiplexer interface that is able to handle both MSX experiments, including ones with overlap.
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#include <MSXDemultiplexer.hpp>
Implementation of the IDemultiplexer interface that is able to handle both MSX experiments, including ones with overlap.
For analyzing overlap data without MSX it is recommended to use the OverlapDemultiplexer instead for better chromatographic interpolation.
Definition at line 31 of file MSXDemultiplexer.hpp.
◆ MSXDemultiplexer()
pwiz::analysis::MSXDemultiplexer::MSXDemultiplexer |
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Params |
p = Params() | ) |
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explicit |
Constructs an MSXDemultiplexer with optional user-specified parameters.
- Parameters
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p | Options to use in demultiplexing (see Params for available options) |
◆ ~MSXDemultiplexer()
virtual pwiz::analysis::MSXDemultiplexer::~MSXDemultiplexer |
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virtual |
◆ Initialize()
◆ BuildDeconvBlock()
Translates a spectrum into a set of matrices to be solved by NNLS.
- Parameters
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[in] | index | Index of the requested spectrum to be demultiplexed |
[in] | muxIndices | The indices to mulitplexed spectra to use for demultiplexing. These spectra should be near in time to the spectrum to demultiplex and there should be enough to provide a unique solution. |
[out] | masks | The design matrix with rows corresponding to individual spectra and columns corresponding to MS1 isolation windows |
[out] | signal | A transition (MS1 isolation -> MS2 point/centroid) to be deconvolved formatted as a column vector (or a set of transitions formatted as a matrix) |
Implements pwiz::analysis::IDemultiplexer.
◆ GetMatrixBlockIndices()
void pwiz::analysis::MSXDemultiplexer::GetMatrixBlockIndices |
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size_t |
indexToDemux, |
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std::vector< size_t > & |
muxIndices, |
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double |
demuxBlockExtra |
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overridevirtual |
Figures out which spectra to include in the system of equations to demux.
This skips over MS1 spectra and returns the indices of a range of MS2 spectra that can be used to demultiplex the chosen spectrum. This handles the case where the chosen spectrum is at the beginning or end of a file and chooses a sufficient number of nearby MS2 spectra accordingly. More indices will be included if the user has chosen to add additional demux blocks.
- Postcondition
- The returned indices are sorted
- Parameters
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[in] | indexToDemux | Index of the requested spectrum |
[out] | muxIndices | Indices of the multiplexed MS2 spectra to be used for demultiplexing |
[in] | demuxBlockExtra | Amount to pad the block size by |
Implements pwiz::analysis::IDemultiplexer.
◆ SpectrumIndices()
const std::vector< size_t > & pwiz::analysis::MSXDemultiplexer::SpectrumIndices |
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const |
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overridevirtual |
Returns the indices to the demultiplexed windows in the solution matrix corresponding to the windows extracted from the spectrum whose index was provided to BuildDeconvBlock()
- Returns
- Returns the demux indices for the solved spectrum
Implements pwiz::analysis::IDemultiplexer.
◆ sl_
◆ pmc_
◆ params_
Params pwiz::analysis::MSXDemultiplexer::params_ |
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private |
◆ spectrumIndices_
std::vector<size_t> pwiz::analysis::MSXDemultiplexer::spectrumIndices_ |
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private |
The documentation for this class was generated from the following file: