Last updated: 2021-09-08

Checks: 6 1

Knit directory: ~/Github/ARIC/

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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: /gpfs/data/im-lab/nas40t2/Data/1000G_hg38_EUR_maf0.01_parquet

# Calculating Covariance

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: /gpfs/data/im-lab/nas40t2/sabrina/ARIC/covariances_1000G_hg38.sh

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


sessionInfo()
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:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] Rcpp_1.0.5       rstudioapi_0.11  knitr_1.30       magrittr_1.5
[5] workflowr_1.6.2  R6_2.4.1         rlang_0.4.8      stringr_1.4.0
[9] tools_4.0.3      xfun_0.18        git2r_0.27.1     htmltools_0.5.0
[13] ellipsis_0.3.1   yaml_2.2.1       digest_0.6.27    rprojroot_1.3-2
[17] tibble_3.0.4     lifecycle_0.2.0  crayon_1.3.4     later_1.1.0.1
[21] vctrs_0.3.4      promises_1.1.1   fs_1.5.0         glue_1.4.2
[25] evaluate_0.14    rmarkdown_2.5    stringi_1.5.3    compiler_4.0.3
[29] pillar_1.4.6     backports_1.1.10 httpuv_1.5.4     pkgconfig_2.0.3