Imputation real allelic R2 user Kantale

Documentation

Computes the R2 (or coefficient of determination) between a real and an imputed genotype.

Parameters

<inputs>
</inputs>

Return

A float value

See also

Imputation Allelic R2 user Kantale, Correlation_user_Kantale

Code

def Imputation_real_allelic_R2_user_Kantale(
	imputed_allele_1 = None,
	imputed_allele_2 = None,
	imputed_gprobs = None,
	real_genotypes = None,
	missing = "0",
):

	if len(imputed_gprobs) != len(real_genotypes):
		raise Exception("Imputed and real gentypes should have equal legth")

	real_values = []
	imputation_values = []
	for real_alleles, gprobs in zip(real_genotypes, imputed_gprobs):
		real_allele_1, real_allele_2 = real_alleles
		
		if real_allele_1 == missing or real_allele_2 == missing:
			continue

		if real_allele_1 == imputed_allele_1 and real_allele_2 == imputed_allele_1:
			real_value = 0.0
		elif (real_allele_1 == imputed_allele_1 and real_allele_2 == imputed_allele_2) or (real_allele_1 == imputed_allele_2 and real_allele_2 == imputed_allele_1):
			real_value = 1.0
		elif real_allele_1 == imputed_allele_2 and real_allele_2 == imputed_allele_2:
			real_value = 2.0
		else:
			#Discordance between REAL and imputed values
			return -1.0

#		imputation_value = (0.0 * gprobs[0]) + (1.0 * gprobs[1]) + (2.0 * gprobs[2])
		imputation_value = gprobs[1] + (2.0 * gprobs[2])

		real_values += [real_value]
		imputation_values += [imputation_value]

	cor = Correlation_user_Kantale(real_values, imputation_values, lib="pyp")
	r2 = cor * cor

	return r2

Unit Tests

def uni1():
	return True

Development Code

def Imputation_real_allelic_R2_user_Kantale():
	pass

Permissions

Documentation Permissions

Kantale

Code Permissions

Kantale

Unit Tests Permissions

Kantale

Permissions Permissions

Kantale