## ----lkb,eval=FALSE-----------------------------------------------------------
# BiocManager::install("PlinkMatrix")

## ----getl, message=FALSE------------------------------------------------------
library(PlinkMatrix)
gdemo <- example_PlinkMatrix()
colnames(gdemo) <- gsub("0_", "", colnames(gdemo))
gdemo

## ----dosan--------------------------------------------------------------------
data(g445samples)
table(g445samples$Population.code)

## ----dopca, message=FALSE-----------------------------------------------------
library(irlba)
set.seed(1234)
ss <- sort(sample(seq_len(nrow(gdemo)), size = 1000))
pca <- prcomp_irlba(t(gdemo[ss, ]), 10)
pairs(pca$x[, 1:4], col = factor(g445samples$Population.code), pch = 19, cex = .5)
boxplot(split(pca$x[, 2] + pca$x[, 1], g445samples$Population.code))

## ----lkra---------------------------------------------------------------------
data(example_GRanges)
library(SummarizedExperiment)
nse <- SummarizedExperiment(list(genotypes = gdemo),
  rowData = example_GRanges, colData = g445samples
)
nse
little <- GenomicRanges::GRanges("chr18:1-100000")
subsetByOverlaps(nse, little)

## ----lksess-------------------------------------------------------------------
sessionInfo()