Pigmentation calculator

[firemonkey]

http://mathgene.usc.es/snipper/skinclassifier.html

Pigmentation.PNG

See http://www.anthrogenica.com/showthre...tion-Predictor . I am surprised an ethnic Turk got 13% more white admixture than me.

[firemonkey]

Updated with one more snp result via FTDNA data

Pigmentation 8.PNG

[RN97]

Wait can u explain how I do this?

[Ashlyn]

It's different every version:

1) 99.68 % for White; 0.32 % for Intermediate; 0.00 % for Black

2) 98.25% White; 1.75% Intermediate; 0.00% Black

3) 91.85% White; 8.15 % Intermediate; 0.00% Black

[Ashlyn]

Wait can u explain how I do this?

Do you have 23&me? Sign in & search your raw data for the following:

RS10777129
RS13289
RS1408799
RS1426654
RS1448484
RS16891982
RS2402130
RS3829241
RS6058017
RS6119471


Use NN for anything that doesn't have info. Enter it here http://mathgene.usc.es/snipper/skinclassifier.html.

[Mortimer]

RS10777129 GG
RS13289 CG
RS1408799 TT (GG)
RS1426654 AG
RS1448484 NN
RS16891982 GG
RS2402130 AA
RS3829241 GG (TT)
RS6058017 NN
RS6119471 NN

GGCGGGAGNNGGAATTNNNN

Naive Bayes (Hardy-Weinberg principle applies)
This profile is 235 times more likely White than Intermediate, and 84,557 times more likely White than Black.

Predicted admixture: 99.57 % for White; 0.42 % for Intermediate; 0.00 % for Black.

Therefore, the profile should be White.

Multinomial logistic regression
Predicted admixture:

White Intermediate Black
0.00 % 100.00 % 0.00 %
This individual is more than a billion (109) times more likely to be Intermediate rather than White.

Therefore, this individual is most likely to be Intermediate.
This individual is more than a billion (109) times more likely to be Intermediate rather than Black.

Therefore, this individual is most likely to be Intermediate.


Genetic distance algorithm
Finally, contributions Cgk sorted in descending order for your profile are:

White 51.21 % Skin colours
Intermediate 27.30 % Skin colours
Black 21.49 %

[Mortimer]

RS10777129 GG
RS13289 CG
RS1408799 TT (GG)
RS1426654 AG
RS1448484 NN
RS16891982 GG
RS2402130 AA
RS3829241 GG (TT)
RS6058017 NN
RS6119471 NN

GGCGGGAGNNGGAATTNNNN

Naive Bayes (Hardy-Weinberg principle applies)
This profile is 235 times more likely White than Intermediate, and 84,557 times more likely White than Black.

Predicted admixture: 99.57 % for White; 0.42 % for Intermediate; 0.00 % for Black.

Therefore, the profile should be White.

Multinomial logistic regression
Predicted admixture:

White Intermediate Black
0.00 % 100.00 % 0.00 %
This individual is more than a billion (109) times more likely to be Intermediate rather than White.

Therefore, this individual is most likely to be Intermediate.
This individual is more than a billion (109) times more likely to be Intermediate rather than Black.

Therefore, this individual is most likely to be Intermediate.


Genetic distance algorithm
Finally, contributions Cgk sorted in descending order for your profile are:

White 51.21 % Skin colours
Intermediate 27.30 % Skin colours
Black 21.49 %

two type of tests say "white" and one says intermediate.

[Mortimer]

Bump. Im curious if any fully european person could get similar results to me especially if any fully european person could get intermediate on

Multinomial logistic regression
Predicted admixture:

White Intermediate Black
0.00 % 100.00 % 0.00 %
This individual is more than a billion (109) times more likely to be Intermediate rather than White.

Therefore, this individual is most likely to be Intermediate.
This individual is more than a billion (109) times more likely to be Intermediate rather than Black.

Therefore, this individual is most likely to be Intermediate.

[firemonkey]

Multinomial logistic regression algorithm.


The likelihoods of your profile are:

White Intermediate Black
1.0478e-91 1.0000e+00 6.4217e-299

Predicted admixture:
White Intermediate Black
0.00 % 100.00 % 0.00 %

This individual is more than a billion (109) times more likely to be Intermediate rather than White.

Therefore, this individual is most likely to be Intermediate.

Performing logistic regression with Intermediate as pivot population...

Loading required package: nnet
# weights: 54 (34 variable)
initial value 120.847352
iter 10 value 9.286072
iter 20 value 3.361739
iter 30 value 3.245533
iter 40 value 3.245360
final value 3.245360
converged
Intermediate Black White
1.000000e+00 6.326099e-162 1.493314e-09
> proc.time()
user system elapsed
0.156 0.021 0.169

The likelihoods of your profile are:
White Intermediate Black
1.4933e-09 1.0000e+00 6.3261e-162

Predicted admixture:
White Intermediate Black
0.00 % 100.00 % 0.00 %

This individual is 669,651,527 times more likely to be Intermediate rather than White.

Therefore, this individual is most likely to be Intermediate.

Performing logistic regression with Black as pivot population...

Loading required package: nnet
# weights: 54 (34 variable)
initial value 120.847352
iter 10 value 13.827990
iter 20 value 3.884220
iter 30 value 3.250048
iter 40 value 3.245373
final value 3.245360
converged
Black Intermediate White
0.000000e+00 1.000000e+00 3.958079e-191
> proc.time()
user system elapsed
0.153 0.020 0.167

The likelihoods of your profile are:
White Intermediate Black
3.9581e-191 1.0000e+00 0.0000e+00

Predicted admixture:
White Intermediate Black
0.00 % 100.00 % 0.00 %

This individual is more than a billion (109) times more likely to be Intermediate rather than White.

Therefore, this individual is most likely to be Intermediate.




Average classification:
White Intermediate Black
0.00 % 100.00 % 0.00 %

This individual is more than a billion (109) times more likely to be Intermediate rather than White.

Therefore, this individual is most likely to be Intermediate.

Genetic distance algorithm

Threshold genetic distance per locus D is 0.67.

Mean genetic distances per locus Dak are:
White 0.64
Intermediate 0.81
Black 0.99


Allele distances White Intermediate Black
White 0.00 0.17 0.34
Intermediate 0.17 0.00 0.18
Black 0.34 0.18 0.00

Genetic relatedness Rak for your profile is:
Black 0.32
Intermediate 0.50
White 0.67

Finally, contributions Cak sorted in descending order for your profile are:
White 54.54 % Skin colours
Intermediate 29.37 % Skin colours
Black 16.09 % Skin colours



Here are the results for the genotype version of the algorithm:


Threshold genetic distance per locus D is 0.67.

Mean genetic distances per locus Dgk are:
White 1.14
Intermediate 1.33
Black 1.44


Genotype distances White Intermediate Black
White 0.00 0.19 0.31
Intermediate 0.19 0.00 0.12
Black 0.31 0.12 0.00

Genetic relatedness Rgk for your profile is:
Black 0.36
Intermediate 0.47
White 0.67

Finally, contributions Cgk sorted in descending order for your profile are:
White 55.49 % Skin colours
Intermediate 26.62 % Skin colours
Black 17.89 % Skin colours

[firemonkey]

See post 53 http://www.anthrogenica.com/showthre...l=1#post316847

My results changing GG for CC.


Pigmentation 8 CC.PNG