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Table 2 Procedure HaplotypeCarrierIdentification(P,C)

From: Predicting haplotype carriers from SNP genotypes in Bos taurus through linear discriminant analysis

Step

Action

1

foreach proportion P and SNP-chip C (7K and 54K) do

2

for n=1100do

3

randomly split the data into 10 subsets of roughly equal size (S={1:10})

 

[10-fold cross-validation]

4

for k=110do

5

use s:sk subsets from S to train the model and subset k for validation;

6

in the training set:

7

- delete monomorphic and collinear SNPs;

7

- select the best combinations of SNPs using BSS until pP SNPs are left;

7

- use BSS-selected SNPs to classify haplotype carriers with LDA;

7

- save SNP discriminant coefficients;

7

- compute the average training error rate;

8

in the validation set:

9

- use BSS-selected SNPs and their discriminant coefficients to classify haplotype carriers;

9

- compute the average validation error rate;