tmp-tests/test-pcadapt.R

In bcm-uga/pcadapt: Fast Principal Component Analysis for Outlier Detection

lfmm <- system.file("extdata", "geno3pops.lfmm", package = "pcadapt")
file.copy(lfmm, tmp <- tempfile(fileext = ".lfmm"))
library(pcadapt)

bed <- pcadapt::read.pcadapt(tmp, type = "lfmm")
# xptr <- pcadapt:::bedXPtr(bed, 150, 1500)

obj.pcadapt <- pcadapt::pcadapt(bed)

bed2 <- pcadapt::read.pcadapt(unclass(bed), type = "bed")
pcadapt(structure(unclass(bed), n = 150, p = 1500, class = "pcadapt_bed"))

str(test <- pcadapt(bed, LD.clumping = TRUE))
sum(is.na(test$loadings[, 1]))
sum(is.na(test$zscores))

plot(test)
plot(test, option = "scores")

obj.svd <- pcadapt::pcadapt(bed, LD.clumping = TRUE, pca.only = TRUE)