Genotyping Uncertainty with Sequencing data - Linkage Disequilibrium
An R package for estimating linkage disequilibrium using low and/or high coverage sequencing data without requiring filtering with respect to read depth.
The easiest way to install GUSMap in R is using the devtools package.
install.packages("devtools") library(devtools) install_github("tpbilton/GUSbase") install_github("tpbilton/GUS-LD")
Note: Some of the functions are coded in C and therefore an appropriate C compiler is needed for the package to work. For windows OS, Rtools (https://cran.r-project.org/bin/windows/Rtools/) provides a compiler.
The best way to understand how to use GUSLD is to read through the Introduction Tutorial contained in the package.
There are plans to contiune developing this package. If you have any suggests for improvement or additional features you like to see, I'd suggest posting a question under the Issues. I'm also happy for people to suggest changes via a pull request provided it fits within the favour of the package.
To cite this R package:
Bilton, T.P., McEwan, J.C., Clarke, S.M., Brauning, R., Van Stijn, T.C., Rowe, S.J., & Dodds, K.G. (2018). Linkage disequilibrium estimation in low coverage high-throughput sequencing data. Genetics, 209(2), 289-400. doi:10.1534/genetics.118.300831
The initial development of this package was partially funded by the Ministry of Business, Innovation and Employment via its funding of the “Genomics for Production & Security in a Biological Economy” programme (Contract ID C10X1306).