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

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 – Normalized Contact map. 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: