These are scripts used for the simulations for the article "Efficient approaches for large-scale GWAS with genotype uncertainty"
They produce data for: Figure 2 Figure 3 Supplementary Figure 1 Supplementary Figure 2 Supplementary Figure 3 and 4 Supplementary Figure 5 and 6 Supplementary Figure 7 and 8 Supplementary Figure 12 Table 2 and 3
It is assumed that the following R-packages are installed (BE AWARE THAT THE CURRENT CODE USES MULTI-THREADING VIA "parallel::mclapply"): parallel SQUAREM
Furthermore that the binaries of "angsd" and "snptest_v2.5.4-beta3" are in the directory, to make these scripts work.
( angsd can be obtained from its github: https://github.com/ANGSD/angsd )
( snptest can be be obtained here: https://www.well.ox.ac.uk/~gav/snptest/#download )\
Example of how to run:
Rscript simulations.R 1000 Rscript simulTable2and3.R 1000 1000 4 1 1.2 1 1000 Rscript plots.R
The "ANGSD-asso" directory holds R code for running ANGSD-asso's latent model and dosage model in R.
#compile with local version of htslib make HTSSRC=../htslib/
#Then recently I have been getting an error (/usr/bin/ld: /home/emil/git/htslib/libhts.a(hfile_s3.o): undefined reference to symbol 'EVP_sha256@@OPENSSL_1_1_0') Can be helped by adding -lcrypto as a LIB (Also see this link: ANGSD/angsd#151 GO TO "Commits")