Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width=4.5,
fig.height=3.5
)
## ----setup--------------------------------------------------------------------
library(future)
library(updog)
data("uitdewilligen")
## -----------------------------------------------------------------------------
refmat <- t(uitdewilligen$refmat)
sizemat <- t(uitdewilligen$sizemat)
ploidy <- uitdewilligen$ploidy
## -----------------------------------------------------------------------------
setdiff(colnames(sizemat), colnames(refmat))
setdiff(rownames(sizemat), rownames(refmat))
## -----------------------------------------------------------------------------
future::availableCores()
## -----------------------------------------------------------------------------
mout <- multidog(refmat = refmat,
sizemat = sizemat,
ploidy = ploidy,
model = "norm",
nc = 2)
## ----eval = FALSE-------------------------------------------------------------
# future::plan(future::multisession, workers = nc)
## ----eval = FALSE-------------------------------------------------------------
# future::plan(future::multicore, workers = 2)
# mout <- multidog(refmat = refmat,
# sizemat = sizemat,
# ploidy = ploidy,
# model = "norm",
# nc = NA)
#
# ## Shut down parallel workers
# future::plan(future::sequential)
## -----------------------------------------------------------------------------
plot(mout, indices = c(1, 5, 100))
## -----------------------------------------------------------------------------
str(mout$snpdf)
## -----------------------------------------------------------------------------
str(mout$inddf)
## -----------------------------------------------------------------------------
genomat <- format_multidog(mout, varname = "geno")
head(genomat)
## -----------------------------------------------------------------------------
dim(mout$snpdf)
dim(mout$inddf)
mout_cleaned <- filter_snp(mout, prop_mis < 0.05 & bias > exp(-1) & bias < exp(1))
dim(mout_cleaned$snpdf)
dim(mout_cleaned$inddf)
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