Documentation for Column.py
¶
Column
¶
Models chromatographic column in an LC-MS process. This is particularly useful to investigate the effect of retention time drifts on chemicals.
CleanColumn
¶
CleanColumn(dataset)
Bases: Column
A clean column with no RT noise
Create a clean column object Args: dataset: the set of Chemicals that passes through this column
Source code in vimms/Column.py
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Column
¶
Column(dataset, noise_sd)
Defines a base Column class that operates on a dataset and having some noise parameter
Create a column object
Parameters:
Name | Type | Description | Default |
---|---|---|---|
dataset
|
the set of Chemicals that passes through this column |
required | |
noise_sd
|
the noise standard deviation sampled from a normal distribution |
required |
Source code in vimms/Column.py
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get_chemical
¶
get_chemical(idx)
Gets the chemical at the specified index (?) Args: idx: the index to search
Returns: the chemical and its offset (?)
Source code in vimms/Column.py
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get_dataset
¶
get_dataset()
Gets a modified dataset with column (RT) noise applied Returns: a new list of Chemicals where its noise have been modified by the column
Source code in vimms/Column.py
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plot_drift
¶
plot_drift()
Plot the drift
Returns: None
Source code in vimms/Column.py
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plot_drift_distribution
¶
plot_drift_distribution()
Plot drift distribution
Returns: None
Source code in vimms/Column.py
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GaussianProcessColumn
¶
GaussianProcessColumn(
dataset, noise_sd, rbf_params, intercept_params, linear_params
)
Bases: Column
A gaussian-process based column
Create a gaussian process drift column Args: dataset: noise_sd: rbf_params: intercept_params: linear_params:
Source code in vimms/Column.py
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LinearColumn
¶
LinearColumn(dataset, noise_sd, intercept_params, linear_params)
Bases: Column
A column with linear drift in the RT
Create a linear drift column Args: dataset: the set of Chemicals that passes through this column noise_sd: noise standard deviation intercept_params: intercept parameters linear_params: linear parameters
Source code in vimms/Column.py
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drift_fn
¶
drift_fn(roi, injection_number)
Drift function
Parameters:
Name | Type | Description | Default |
---|---|---|---|
roi
|
|
required | |
injection_number
|
|
required |
Returns: ???
Source code in vimms/Column.py
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from_fixed_offsets
staticmethod
¶
from_fixed_offsets(dataset, noise_sd, intercept_term, linear_term)
From fixed offsets
Parameters:
Name | Type | Description | Default |
---|---|---|---|
dataset
|
|
required | |
noise_sd
|
|
required | |
intercept_term
|
|
required | |
linear_term
|
|
required |
Returns: ???
Source code in vimms/Column.py
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