README.md

In eriqande/fullsniplings: Full sibling reconstruction from SNP data

fullsniplings

An R package to infer full-sibling relationships from genetic data. Geared toward datasets with many individuals and about 100 SNPs which are treated as if they are unlinked. (While that is clearly false, it might be reasonable). The method is based on computing the posterior predictive distribution of genotypes conditional on currently-inferred sibling groups. I will eventually generalize that to more general pedigree inference, but for now just want to implement the easy full-sibling case as a prototypical exercise.

Installing / Building

On a Mac you need to have the developer command line tools, and on a PC you will want the RTools to build this package. You need to have the Rcpp package as well, and also the devtools package. You can get both of those from CRAN.

Here is what you would do:

# download, build and install the package
devtools::install_github(repo="fullsniplings", username="eriqande")

Running a Simple Data set

Take a look at the first few lines of a SNP data set that has 1157 Chinook typed at 95 SNPs:

head(fs_dev_test_data$chinook_full_sibs_genos)

It is simple two column format (each locus gets two alleles) with the rownames being the IDs of the fish. Missing data are denote by NA, as is typical in R.

The main function for running the MCMC is run_mcmc. It is not fully documented, yet, but you can do:

?run_mcmc

to learn about it. The example shows how to do a short run.

If you want to do a longer run (about 5 minutes) you can do

quick_run  <- run_mcmc(fs_dev_test_data$chinook_full_sibs_genos, burn_in = 50, num_sweeps = 200)

Building a vignette that shows how I used fullsniplings for my talk at the Coastwide meeting in June of 2014

To do this, you will need V2 of the rmarkdown package. You can get that either by using the latest preview version of Rstudio: http://www.rstudio.com/products/rstudio/download/preview/ or by installing rmarkdown from github like this:

devtools::install_github("eriqande/fullsniplings")

Then, once you have done that you should be able to do

rmarkdown::render(system.file("dev_vignettes/full-sibling-chinook-mcmc.Rmd", package="fullsniplings"), output_format = "html_document", output_file = "~/full-sibling-chinook-mcmc.html")

That will put the output in your home directory in the file full-sibling-chinook-mcmc.html as long as your system recognizes the ~. If not, just put an absolute path of your choice in for the output_file parameter in the render function.

Note that this doesn't run the MCMC, it just grabs some stored results. But you can go into the code of

system.file("dev_vignettes/full-sibling-chinook-mcmc.Rmd", package="fullsniplings")

and uncomment the appropriate lines to run it all.

eriqande/fullsniplings documentation built on May 16, 2019, 8:45 a.m.