def computeRealizedRelationshipKernel(self,genotype=None):
X = zeroMeanUnitVarianz(data=genotype)
K = 1.0/X.shape[1]*sp.dot(X,X.T)
#if K contains negative values set these values to 0
ind = sp.where(K<0)
K[ind] = 0
return K
def computeRealizedRelationshipKernel(self, genotype=None):
X = zeroMeanUnitVarianz(data=genotype)
K = 1.0 / X.shape[1] * sp.dot(X, X.T)
#if K contains negative values set these values to 0
ind = sp.where(K < 0)
K[ind] = 0
return K
def transformData(self,data=None,transformation="none"):
data = data.flatten()
if transformation=="zeroMean":
return zeroMean(data)
elif transformation=="unitVariance":
return zeroMeanUnitVarianz(data)
elif transformation=="sqrt":
return sqrtTransformation(data)
elif transformation=="log10":
return logTransformation(data)
elif transformation=="boxcox":
new_data = boxcoxTransformation(data)
if new_data.sum()==data.sum():
self.__transformed = False
else:
self.__transformed = True
return new_data
elif transformation=="dummyVariable":
return createDummyVariables(data)
else:
return data
def transformData(self, data=None, transformation="none"):
data = data.flatten()
if transformation == "zeroMean":
return zeroMean(data)
elif transformation == "unitVariance":
return zeroMeanUnitVarianz(data)
elif transformation == "sqrt":
return sqrtTransformation(data)
elif transformation == "log10":
return logTransformation(data)
elif transformation == "boxcox":
new_data = boxcoxTransformation(data)
if new_data.sum() == data.sum():
self.__transformed = False
else:
self.__transformed = True
return new_data
elif transformation == "dummyVariable":
return createDummyVariables(data)
else:
return data