Last updated: 2021-09-08

Checks: 6 1

Knit directory: ~/Github/ARIC/

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Download Data takes genotypes in parquet format. Run git clone The data can be downloaded: Or in CRI: /gpfs/data/im-lab/nas40t2/Data/1000G_hg38_EUR_maf0.01_parquet

Calculating Covariance


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/

python $CODE/ \
-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

[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