sHWE {lfa} | R Documentation |
Compute structural Hardy-Weinberg Equilibrium (sHWE) p-values on a SNP-by-SNP basis. These p-values can be aggregated to determine genome-wide goodness-of-fit for a particular value of d. See https://doi.org/10.1101/240804 for more details.
sHWE(X, LF, B)
X |
a matrix of SNP genotypes, i.e. an integer matrix of 0's, 1's, and 2's. Sparse matrices of class Matrix are not supported (yet). |
LF |
matrix of logistic factors |
B |
number of null datasets to generate - B=1 is usualy sufficient. If computational time/power allows, a few extra B could be helpful |
a vector of p-values for each SNP.
LF <- lfa(hgdp_subset, 4) gof_4 <- sHWE(hgdp_subset, LF, 3) LF <- lfa(hgdp_subset, 10) gof_10 <- sHWE(hgdp_subset, LF, 3) hist(gof_4) hist(gof_10)