model.gof-deprecated: LFA model goodness of fit

In StoreyLab/lfa: Logistic Factor Analysis for Categorical Data

LFA model goodness of fit

Description

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.

Usage

model.gof(X, LF, B)

Arguments

X	A matrix of SNP genotypes, i.e. an integer matrix of 0's, 1's, 2's and NAs. BEDMatrix is supported.
LF	matrix of logistic factors
B	number of null datasets to generate, B = 1 is usually sufficient. If computational time/power allows, a few extra B could be helpful

Details

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

Value

vector of p-values for each SNP.

Note

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.

See Also

lfa-deprecated()

StoreyLab/lfa documentation built on March 7, 2024, 9:59 p.m.