model.gof-deprecated | R Documentation |

Compute SNP-by-SNP goodness-of-fit when compared to population
structure. This can be aggregated to determine genome-wide
goodness-of-fit for a particular value of `d`

.

model.gof(X, LF, B)

`X` |
A matrix of SNP genotypes, i.e. an integer matrix of 0's,
1's, 2's and |

`LF` |
matrix of logistic factors |

`B` |
number of null datasets to generate, |

This function returns p-values for LFA model goodness of fit based on a simulated null.

vector of p-values for each SNP.

Genotype matrix is expected to be a matrix of integers with values 0, 1, and 2. Currently no support for missing values. Note that the coding of the SNPs does not affect the algorithm.

`lfa-deprecated()`

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