All three links to the examples are broken

[sam0per]

Hi there,

I was curious to see how to use your package but all the three links pasted in your README are broken.
What I am particularly interested in is the function beta2genotype which is supposed to convert methylation beta-values into genotypes. However, what I do not understand/used to is the use of genotypes in the form of 1, 2 and 3. Are these the same as 0, 1 and 2 and so 1 = 0, 2 = 1 and 3 = 2?

Cheers.

[DavyCats]

You can find a vignette on the bioconductor page: https://bioconductor.org/packages/release/bioc/html/omicsPrint.html.

With regards to the genotype encoding: Yes, essentially 1,2,3 is the same as 0,1,2. One thing to note though is that the beta2genotype function assigns these values based on the beta values, so high methylation of a probe (linked to an SNP) would result in a value of 3 and lower would result in 1. These values, therefore, don't strictly refer to reference or alternative alleles, like they might for DNA based genotypes, as this will depend on what the effect of the SNP on methylation is. The alleleSharing function has some functionality to cope with this (you can enable this by setting the alignment parameter to TRUE).

[sam0per]

Alright, thanks but it is still not very clear to me how a SNP may determine a genotype 1,2 or 3. In the vignette of the bioconductor page, it says

Several additional vignettes are available that show the use of the package on further experimental data in different settings, i.e., 450k DNA methylation and imputed genotypes.

Would you mind sharing these additional vignettes so that I can understand better how these genotypes depend on methylation and SNPs please?

[DavyCats]

There are some other vignettes available here: https://github.com/molepi/omicsPrint/tree/examples/examples (that's on the examples branch).