Last updated: 2022-04-17

Checks: 5 2

Knit directory: cTWAS_analysis/

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    Ignored:    data/AF/

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    Modified:   analysis/SCZ_Cross_Tissue_Analysis.Rmd

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Weight QC

#number of imputed weights
nrow(qclist_all)
[1] 9809
#number of imputed weights by chromosome
table(qclist_all$chr)

  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20 
968 704 572 395 453 573 498 359 366 394 599 571 207 337 341 396 606 157 750 301 
 21  22 
 25 237 
#number of imputed weights without missing variants
sum(qclist_all$nmiss==0)
[1] 6827
#proportion of imputed weights without missing variants
mean(qclist_all$nmiss==0)
[1] 0.696

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8        highr_0.9         jquerylib_0.1.4   compiler_3.6.1   
 [5] pillar_1.6.4      later_0.8.0       git2r_0.26.1      tools_3.6.1      
 [9] getPass_0.2-2     bit_4.0.4         digest_0.6.29     memoise_2.0.1    
[13] RSQLite_2.2.8     evaluate_0.14     tibble_3.1.6      lifecycle_1.0.1  
[17] pkgconfig_2.0.3   rlang_1.0.1       DBI_1.1.2         cli_3.1.0        
[21] rstudioapi_0.13   yaml_2.2.1        xfun_0.29         fastmap_1.1.0    
[25] httr_1.4.2        stringr_1.4.0     knitr_1.36        fs_1.5.2         
[29] vctrs_0.3.8       bit64_4.0.5       rprojroot_2.0.2   data.table_1.14.2
[33] glue_1.6.2        R6_2.5.1          processx_3.5.2    fansi_1.0.2      
[37] rmarkdown_2.11    blob_1.2.2        callr_3.7.0       magrittr_2.0.2   
[41] whisker_0.3-2     ps_1.6.0          promises_1.0.1    htmltools_0.5.2  
[45] ellipsis_0.3.2    httpuv_1.5.1      utf8_1.2.2        stringi_1.7.6    
[49] cachem_1.0.6      crayon_1.5.0