Utility Functions¶
This section describes the main utility function parameters (which may be of interest to advanced users).
The utilities
module provides convenience functions for working with profiling datasets.

nPYc.utilities.
rsd
(data)¶ Calculate percentage relative standard deviation for each column in data.
\(\mathit{{rsd(x)}} = \frac{\mathit{\sigma_{x}}}{\mathit{\mu_{x}}} \times 100\)
Where RSDs cannot be calculated, (i.e. means of zero),
numpy.finfo(numpy.float64).max
is returned.Parameters: data (numpy.ndarray) – n by m numpy array of data, with features in columns, and samples in rows Returns: m vector of RSDs Return type: numpy.ndarray

nPYc.utilities.
buildFileList
(filepath, pattern)¶ Search for data files, by attempting to match to the file path regex pattern. :param filepath: Look for data in all the directories under this location :type searchDirectory: str :param pattern: Recognise experimental data by matching path to this compiled regex :type pattern: re.SRE_Pattern :return: A list of all paths below searchDirectory that matched pattern :rtype: list[str,]

nPYc.utilities.
sequentialPrecision
(data)¶ Calculate percentage sequential precision for each column in data. Sequential precision for feature \(x\) is defined as:
\(\mathit{{sp(x)}} = \frac{\sqrt{(\frac{1}{n1} \sum_{i=1}^{n1} (x_{i+1}  x_i)^2)/2}}{\mu_{x}} \times 100\)
Parameters: data (numpy.ndarray) – n by m numpy array of measures, with features in columns, and samples in rows Returns: m vector of sequential precision measures Return type: numpy.ndarray

nPYc.utilities.
rsdsBySampleType
(dataset, onlyPrecisionReferences=True, useColumn='SampleType')¶ Return percent RSDs calculated for the distinct class values in useColumn, defaults to the SampleType enums in ‘SampleType’.
Parameters:  dataset (Dataset) – Dataset object to generate RSDs for.
 onlyPrecisionReferences (bool) – If
True
only use samples with the ‘AssayRole’ PrecisionReference
Returns: Dict of RSDs for each group
Return type: dict(str:numpy array)