PyPop.Homozygosity#
Module for calculating homozygosity statistics.
Classes#
Calculate homozygosity statistics. |
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Calculate homozygosity statistics. |
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Functions#
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Module Contents#
- getObservedHomozygosityFromAlleleData(alleleData)#
- class Homozygosity(alleleData, rootPath='.', debug=0)#
Calculate homozygosity statistics.
Given allele count data for a given locus, calculates the observed homozygosity and returns the approximate expected homozygosity statistics taken from previous simulation runs.
Constructor for homozygosity statistics.
Given:
‘alleleCountData’: tuple consisting of a dictionary of alleles with their associated counts and the total number of alleles.
‘rootPath’: path to the root of the directory where the pre-calculated expected homozygosity statistics can be found.
‘debug’: flag to switch debugging on.
- getObservedHomozygosity()#
Calculate and return observed homozygosity.
Available even if expected stats cannot be calculated
- canGenerateExpectedStats()#
Can expected homozygosity stats be calculated?
Returns true if expected homozygosity statistics can be calculated. Should be called before attempting to get any expected homozygosity statistics.
- getPValueRange()#
Gets lower and upper bounds for p-value.
Returns a tuple of (lower, upper) bounds.
Only meaningful if ‘canGenerateExpectedStats()’ returns true.
- getCount()#
Number of runs used to calculate statistics.
Only meaningful if ‘canGenerateExpectedStats()’ returns true.
- getExpectedHomozygosity()#
Gets mean of expected homozygosity.
This is the estimate of the expected homozygosity.
Only meaningful if ‘canGenerateExpectedStats()’ returns true.
- getVarExpectedHomozygosity()#
Gets variance of expected homozygosity.
This is the estimate of the variance expected homozygosity.
Only meaningful if ‘canGenerateExpectedStats()’ returns true.
- getNormDevHomozygosity()#
Gets normalized deviate of homozygosity.
Only meaningful if ‘canGenerateExpectedStats()’ returns true.
- serializeHomozygosityTo(stream)#
- class HomozygosityEWSlatkinExact(alleleData=None, numReplicates=10000, debug=0)#
Bases:
Homozygosity
Calculate homozygosity statistics.
Given allele count data for a given locus, calculates the observed homozygosity and returns the approximate expected homozygosity statistics taken from previous simulation runs.
Constructor for homozygosity statistics.
Given:
‘alleleCountData’: tuple consisting of a dictionary of alleles with their associated counts and the total number of alleles.
‘rootPath’: path to the root of the directory where the pre-calculated expected homozygosity statistics can be found.
‘debug’: flag to switch debugging on.
- doCalcs(alleleData)#
- getHomozygosity()#
- serializeHomozygosityTo(stream)#
- returnBulkHomozygosityStats(alleleCountDict=None, binningMethod=None)#