Fit updog

Load updog and the snpdat dataset. The data frame snpdat contains three example SNPs (single nucleotide polymorphisms) from the study of Shirasawa et al. (2017). The individuals in this dataset resulted from a single generation of selfing (an S1 population). You can read more about it by typing ?snpdat.

set.seed(1)
library(updog)
data("snpdat")

We’ll extract the First SNP.

smalldat <- snpdat[snpdat$snp == "SNP1", c("counts", "size", "id")]
head(smalldat)
#> # A tibble: 6 × 3
#>   counts  size id           
#>    <int> <int> <chr>        
#> 1    298   354 Xushu18      
#> 2    187   187 Xushu18S1-001
#> 3    201   201 Xushu18S1-002
#> 4    157   184 Xushu18S1-003
#> 5    175   215 Xushu18S1-004
#> 6    283   283 Xushu18S1-005

We will separate the counts between the children and the parent (the first individual). Note that you do not need the parental counts to fit updog, but they can help improve estimates of the parameters in the updog model.

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

We can first use plot_geno to visualize the raw data.

plot_geno(refvec = oref, sizevec = osize, ploidy = ploidy)

Now we use the flexdog function to fit the model. We use model = "s1" because the individuals resulted from one generation of selfing of the same parent.

uout <- flexdog(refvec  = oref, 
                sizevec = osize, 
                ploidy  = ploidy, 
                model   = "s1", 
                p1ref   = pref, 
                p1size  = psize)
#>          Fit: 1 of 5 
#> Initial Bias: 0.3678794 
#> Log-Likelihood: -592.9506 
#> Keeping new fit.
#> 
#>          Fit: 2 of 5 
#> Initial Bias: 0.6065307 
#> Log-Likelihood: -592.9506 
#> Keeping old fit.
#> 
#>          Fit: 3 of 5 
#> Initial Bias: 1 
#> Log-Likelihood: -538.1967 
#> Keeping new fit.
#> 
#>          Fit: 4 of 5 
#> Initial Bias: 1.648721 
#> Log-Likelihood: -538.1963 
#> Keeping new fit.
#> 
#>          Fit: 5 of 5 
#> Initial Bias: 2.718282 
#> Log-Likelihood: -538.1963 
#> Keeping old fit.
#> 
#> Done!

Analyze Output

We use plot.flexdog to visualize the fit. Points are color coded according to the genotype with the highest posterior probability. For example, a genotype of “4” represents four copies of the reference allele and two copies of the alternative allele (AAAAaa). The level of transparency is proportional to the maximum posterior probability. This is equivalent to the posterior probability that this genotype estimate is correct. The lines represent the mean counts at a given genotype. The “+” symbol with a black dot is the location of the parent.

plot(uout)

Filtering SNPs

For downstream analyses, you might want to filter out poorly behaved SNPs. These SNPs might be poorly behaved for a variety of reasons (they might not be real SNPs, it might be much more very difficult to map one allele to the correct location relative to the other allele, etc). Updog gives you some measures to filter out these SNPs.

The most intuitive measure would be the (posterior) proportion of individuals mis-genotyped:

uout$prop_mis
#> [1] 0.04216399

For this SNP, we expect about 4.22 percent of the individuals to be mis-genotyped. The specific cutoff you use is context and data dependent. But as a starting point, you could try a loose cutoff by keeping SNPs only if they have a prop_mis of less than 0.2.

From our simulation studies, we also generally get rid of SNPs with overdispersion parameters greater than 0.05 or SNPs with bias parameters either less than 0.5 or greater than 2. However, if you have higher or lower read depths than what we looked at in our simulations, you should adjust these levels accordingly.