smells_like_updog.R
In updog: Flexible Genotyping for Polyploids

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width=4.5, 
  fig.height=3.5
)

## ----message=FALSE------------------------------------------------------------
set.seed(1)
library(updog)
data("snpdat")

## ----message=FALSE------------------------------------------------------------
smalldat <- snpdat[snpdat$snp == "SNP1", c("counts", "size", "id")]
head(smalldat)

## -----------------------------------------------------------------------------
pref    <- smalldat$counts[1]
psize   <- smalldat$size[1]
oref    <- smalldat$counts[-1]
osize   <- smalldat$size[-1]
ploidy  <- 6 # sweet potatoes are hexaploid

## ----warning=FALSE------------------------------------------------------------
plot_geno(refvec = oref, sizevec = osize, ploidy = ploidy)

## -----------------------------------------------------------------------------
uout <- flexdog(refvec  = oref, 
                sizevec = osize, 
                ploidy  = ploidy, 
                model   = "s1", 
                p1ref   = pref, 
                p1size  = psize)

## -----------------------------------------------------------------------------
plot(uout)

## -----------------------------------------------------------------------------
uout$prop_mis