Binomial(n, p) scaling
Binomial(n, p) scaling where n is fixed and p is estimated.
snp_scaleAlpha(alpha = -1) snp_scaleBinom(nploidy = 2)
alpha |
Assumes that the average contribution (e.g. heritability)
of a SNP of frequency p is proportional to
[2p(1-p)]^{1+α}. The |
nploidy |
Number of trials, parameter of the binomial distribution.
Default is |
You will probably not use this function as is but as the
fun.scaling parameter of other functions of package bigstatsr.
A new function that returns a data.frame of two vectors
"center" and "scale" which are of the length of ind.col.
This scaling is widely used for SNP arrays. Patterson N, Price AL, Reich D (2006). Population Structure and Eigenanalysis. PLoS Genet 2(12): e190. doi: 10.1371/journal.pgen.0020190.
set.seed(1) a <- matrix(0, 93, 170) p <- 0.2 a[] <- rbinom(length(a), 2, p) X <- add_code256(big_copy(a, type = "raw"), code = c(0, 1, 2, rep(NA, 253))) X.svd <- big_SVD(X, fun.scaling = snp_scaleBinom()) str(X.svd) plot(X.svd$center) abline(h = 2 * p, col = "red") plot(X.svd$scale) abline(h = sqrt(2 * p * (1 - p)), col = "red")
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