corrMatrix module¶
corrMatrix.calculateCorrMatrix (…[, maskvalue]) |
Calculate correlation matrix from a 2D numpy array. |
corrMatrix.calculateCovMatrix (…[, maskvalue]) |
Calculate covariance matrix from a 2D numpy array. |
corrMatrix.calculateCorrelation (ndarray x, …) |
Calculate correlation between two 1D numpy array. |
corrMatrix.calculateCovariance (ndarray x, …) |
Calculate covariance between two 1D numpy array. |
corrMatrix.calculateCorrMatrixForCCMap (…) |
Calculate correlation matrix of a contact map. |
corrMatrix.calculateCorrMatrixForGCMaps (…) |
Calculate Correlation matrix for all maps present in input gcmap file It calculates correlation between all rows and columns of contact map. |
-
calculateCorrMatrix
(ndarray in_array, ndarray out=None, maskvalue=None)¶ Calculate correlation matrix from a 2D numpy array. During calculation, array values equal to maskvalue will not be considered.
Parameters: - in_array (numpy.ndarray) – Input numpy array
- out (numpy.ndarray) – If it is
None
, output array is returned. - maskvalue (float) – If this value is given, all elements of input array with this equal value is masked during the calculation.
Returns: out – In case of
out=None
, ouput array will be returned. Otherwise,None
is returnedReturn type: numpy.ndarray or None
-
calculateCovMatrix
(ndarray in_array, ndarray out=None, maskvalue=None)¶ Calculate covariance matrix from a 2D numpy array. During calculation, array values equal to maskvalue will not be considered.
Parameters: - in_array (numpy.ndarray) – Input numpy array
- out (numpy.ndarray) – If it is
None
, output array is returned. - maskvalue (float) – If this value is given, all elements of input array with this equal value is masked during the calculation.
Returns: out – In case of
out=None
, ouput array will be returned. Otherwise,None
is returnedReturn type: numpy.ndarray or None
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calculateCorrelation
(ndarray x, ndarray y, maskvalue=None)¶ Calculate correlation between two 1D numpy array. During calculation, array values equal to maskvalue will not be considered.
Parameters: - x (numpy.ndarray) – First input numpy array
- y (numpy.ndarray) – Second input numpy array
- maskvalue (float) – If this value is given, all elements of input array with this equal value is masked during the calculation.
Returns: result – Correlation coefficient
Return type:
-
calculateCovariance
(ndarray x, ndarray y, maskvalue=None)¶ Calculate covariance between two 1D numpy array. During calculation, array values equal to maskvalue will not be considered.
Parameters: - x (numpy.ndarray) – First input numpy array
- y (numpy.ndarray) – Second input numpy array
- maskvalue (float) – If this value is given, all elements of input array with this equal value is masked during the calculation.
Returns: result – Covariance value
Return type:
-
calculateCorrMatrixForCCMap
(inputCCMap, logspace=False, maskvalue=0.0, vmin=None, vmax=None, outFile=None, workDir=None)¶ Calculate correlation matrix of a contact map. It calculates correlation between all rows and columns of contact map.
Parameters: - ccMap (
gcMapExplorer.lib.ccmap.CCMAP
or ccmap file) – A CCMAP object containing observed contact frequency or a ccmap file. - logspace (bool) – If its value is
True
, at first map is converted as logarithm of map and subsequently correlation will be calculated. - maskvalue (float) – Do not consider bins with this value during calculation. By default here it is zero because bins with zero is considered to be have missing data.
- vmin (float) – Minimum threshold value for normalization. If contact frequency is less than or equal to this threshold value, this value is discarded during normalization.
- vmax (float) – Maximum threshold value for normalization. If contact frequency is greater than or equal to this threshold value, this value is discarded during normalization.
- outFile (str) – Name of output ccmap file, to save directly the correlation matrix as a ccmap file.
In case of this option,
None
will return. - workDir (str) – Path to the directory where temporary intermediate files are generated.
If
None
, files are generated in the temporary directory according to the main configuration.
Returns: ccMapObj – Correlation matrix as ccmap object. When
outFile
is provided,None
is returned. In case of any other error,None
is returned.Return type: gcMapExplorer.lib.ccmap.CCMAP
orNone
- ccMap (
-
calculateCorrMatrixForGCMaps
(gcMapInputFile, gcMapOutFile, logspace=False, maskvalue=0.0, vmin=None, vmax=None, replaceMatrix=False, compression='lzf', workDir=None)¶ Calculate Correlation matrix for all maps present in input gcmap file It calculates correlation between all rows and columns of contact map.
Parameters: - gcMapInputFile (str) – Input gcmap file.
- gcMapOutFile (str) – Output gcmap file.
- logspace (bool) – If its value is
True
, at first map is converted as logarithm of map and subsequently correlation will be calculated. - maskvalue (float) – Do not consider bins with this value during calculation. By default here it is zero because bins with zero is considered to be have missing data.
- vmin (float) – Minimum threshold value for normalization. If contact frequency is less than or equal to this threshold value, this value is discarded during normalization.
- vmax (float) – Maximum threshold value for normalization. If contact frequency is greater than or equal to this threshold value, this value is discarded during normalization.
- replaceMatrix (bool) – If its value is
True
, the map will be replaced in output file. Otherwise, if a map is present, calculation will be skipped. - compression (str) – Compression method in output gcmap file. Presently allowed :
lzf
for LZF compression andgzip
for GZIP compression. - workDir (str) – Path to the directory where temporary intermediate files are generated.
If
None
, files are generated in the temporary directory according to the main configuration.
Returns: Return type: