Last updated: 2021-09-08
Checks: 6 1
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Untracked files: Untracked: .DS_Store Untracked: .Rhistory Untracked: ARIC_EA_hg38_validation.Rmd Untracked: ARIC_EA_hg38_validation.html Untracked: ARIC_EA_hg38_validation_height.Rmd Untracked: ARIC_EA_hg38_validation_height.html Untracked: PWAS/ Untracked: code/ Untracked: covariances_EA_hg38.Rmd Untracked: figure/ Untracked: models/ Untracked: results/ Untracked: test_data/ Untracked: weights_EA.Rmd Untracked: weights_EA.html
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covariance_for_model.py takes genotypes in parquet format. Run
git clone https://github.com/hakyimlab/summary-gwas-imputation.git. The data can be downloaded: https://zenodo.org/record/3569954#.XyRiqChKiUk. Or in CRI:
CODE=/Users/t.med.scmi/Github/summary-gwas-imputation DATA=/gpfs/data/im-lab/nas40t2/Data/1000G_hg38_EUR_maf0.01_parquet MODEL=/gpfs/data/im-lab/nas40t2/sabrina/ARIC
parquet_genotype_pattern helps identify genotype files by chromosome.
ARIC_EA_hg38.db is a PrediXcan format prediction model defined in hg38. The script can also be submitted as a job in CRI:
python $CODE/covariance_for_model.py \ -parquet_genotype_folder $DATA \ -parquet_genotype_pattern "chr(.*).variants.parquet" \ -model_db $MODEL/ARIC_EA_hg38.db \ -output $MODEL/ARIC_EA_hg38.txt.gz \ -parsimony 1
R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached):  Rcpp_1.0.5 rstudioapi_0.11 knitr_1.30 magrittr_1.5  workflowr_1.6.2 R6_2.4.1 rlang_0.4.8 stringr_1.4.0  tools_4.0.3 xfun_0.18 git2r_0.27.1 htmltools_0.5.0  ellipsis_0.3.1 yaml_2.2.1 digest_0.6.27 rprojroot_1.3-2  tibble_3.0.4 lifecycle_0.2.0 crayon_1.3.4 later_126.96.36.199  vctrs_0.3.4 promises_1.1.1 fs_1.5.0 glue_1.4.2  evaluate_0.14 rmarkdown_2.5 stringi_1.5.3 compiler_4.0.3  pillar_1.4.6 backports_1.1.10 httpuv_1.5.4 pkgconfig_2.0.3