The makesigmasemiPDRcppGSL was r package for marsR to compute the positive semidefinite of LD matrix.
- The C++ library for GNU GSL is required.
- makesigmasemiPDRcppGSL works only on *nix (Linux, Unix such as macOS) system. please check .Platform$OS.type function.
- We currently only support R 3.5+.*
install.packages("Rcpp")
install.packages("RcppGSL")
install.packages("devtools")
devtools::install_github("junghyunJJ/makesigmasemiPDRcppGSL")
> library(makesigmasemiPDRcppGSL)
> data("testdata")
> dim(testdata$geno)
[1] 471 489
> testdata$geno[1:5,1:5]
sample1 sample2 sample3 sample4 sample5
rs1 1 1 1 1 2
rs2 0 0 0 0 0
rs3 0 1 0 0 0
rs4 0 1 0 0 0
rs5 0 1 0 0 0
> res <- makesigmasemiPDRcppGSL(testdata$geno)
> dim(res)
[1] 471 471
> res[1:5,1:5]
[,1] [,2] [,3] [,4] [,5]
[1,] 1.10000000 0.31751143 -0.30376036 0.09944961 0.09944961
[2,] 0.31751143 1.10000000 -0.07018644 -0.08088798 -0.08088798
[3,] -0.30376036 -0.07018644 1.10000000 -0.03654935 -0.03654935
[4,] 0.09944961 -0.08088798 -0.03654935 1.10000000 1.00000000
[5,] 0.09944961 -0.08088798 -0.03654935 1.00000000 1.10000000