Last updated: 2022-03-06

Checks: 5 2

Knit directory: cTWAS_analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

The command set.seed(20211220) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

Using absolute paths to the files within your workflowr project makes it difficult for you and others to run your code on a different machine. Change the absolute path(s) below to the suggested relative path(s) to make your code more reproducible.

absolute relative
/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/ data
/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/code/ctwas_config.R code/ctwas_config.R

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 4c71b11. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .ipynb_checkpoints/
    Ignored:    data/AF/

Untracked files:
    Untracked:  Rplot.png
    Untracked:  analysis/.ipynb_checkpoints/
    Untracked:  analysis/SCZ_Cross_Tissue_Analysis.Rmd
    Untracked:  code/.ipynb_checkpoints/
    Untracked:  code/AF_out/
    Untracked:  code/Autism_out/
    Untracked:  code/BMI_S_out/
    Untracked:  code/BMI_out/
    Untracked:  code/Glucose_out/
    Untracked:  code/LDL_S_out/
    Untracked:  code/SCZ_S_out/
    Untracked:  code/SCZ_out/
    Untracked:  code/T2D_out/
    Untracked:  code/ctwas_config.R
    Untracked:  code/mapping.R
    Untracked:  code/out/
    Untracked:  code/run_AF_analysis.sbatch
    Untracked:  code/run_AF_analysis.sh
    Untracked:  code/run_AF_ctwas_rss_LDR.R
    Untracked:  code/run_Autism_analysis.sbatch
    Untracked:  code/run_Autism_analysis.sh
    Untracked:  code/run_Autism_ctwas_rss_LDR.R
    Untracked:  code/run_BMI_analysis.sbatch
    Untracked:  code/run_BMI_analysis.sh
    Untracked:  code/run_BMI_analysis_S.sbatch
    Untracked:  code/run_BMI_analysis_S.sh
    Untracked:  code/run_BMI_ctwas_rss_LDR.R
    Untracked:  code/run_BMI_ctwas_rss_LDR_S.R
    Untracked:  code/run_Glucose_analysis.sbatch
    Untracked:  code/run_Glucose_analysis.sh
    Untracked:  code/run_Glucose_ctwas_rss_LDR.R
    Untracked:  code/run_LDL_analysis_S.sbatch
    Untracked:  code/run_LDL_analysis_S.sh
    Untracked:  code/run_LDL_ctwas_rss_LDR_S.R
    Untracked:  code/run_SCZ_analysis.sbatch
    Untracked:  code/run_SCZ_analysis.sh
    Untracked:  code/run_SCZ_analysis_S.sbatch
    Untracked:  code/run_SCZ_analysis_S.sh
    Untracked:  code/run_SCZ_ctwas_rss_LDR.R
    Untracked:  code/run_SCZ_ctwas_rss_LDR_S.R
    Untracked:  code/run_T2D_analysis.sbatch
    Untracked:  code/run_T2D_analysis.sh
    Untracked:  code/run_T2D_ctwas_rss_LDR.R
    Untracked:  code/wflow_build.R
    Untracked:  code/wflow_build.sbatch
    Untracked:  data/.ipynb_checkpoints/
    Untracked:  data/BMI/
    Untracked:  data/SCZ/
    Untracked:  data/SCZ_S/
    Untracked:  data/T2D/
    Untracked:  data/UKBB/
    Untracked:  data/UKBB_SNPs_Info.text
    Untracked:  data/gene_OMIM.txt
    Untracked:  data/gene_pip_0.8.txt
    Untracked:  data/mashr_Heart_Atrial_Appendage.db
    Untracked:  data/mashr_sqtl/
    Untracked:  data/summary_known_genes_annotations.xlsx
    Untracked:  data/untitled.txt

Unstaged changes:
    Modified:   analysis/SCZ_Brain_Amygdala.Rmd
    Modified:   analysis/SCZ_Brain_Anterior_cingulate_cortex_BA24.Rmd
    Modified:   analysis/SCZ_Brain_Caudate_basal_ganglia.Rmd
    Modified:   analysis/SCZ_Brain_Cerebellar_Hemisphere.Rmd
    Modified:   analysis/SCZ_Brain_Cerebellum.Rmd
    Modified:   analysis/SCZ_Brain_Cortex.Rmd
    Modified:   analysis/SCZ_Brain_Frontal_Cortex_BA9.Rmd
    Modified:   analysis/SCZ_Brain_Hippocampus.Rmd
    Modified:   analysis/SCZ_Brain_Hypothalamus.Rmd
    Modified:   analysis/SCZ_Brain_Nucleus_accumbens_basal_ganglia.Rmd
    Modified:   analysis/SCZ_Brain_Putamen_basal_ganglia.Rmd
    Modified:   analysis/SCZ_Brain_Spinal_cord_cervical_c-1.Rmd
    Modified:   analysis/SCZ_Brain_Substantia_nigra.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the repository in which changes were made to the R Markdown (analysis/SCZ_Brain_Spinal_cord_cervical_c-1.Rmd) and HTML (docs/SCZ_Brain_Spinal_cord_cervical_c-1.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd 4c71b11 sq-96 2022-03-05 update
html 4c71b11 sq-96 2022-03-05 update
Rmd 4a5db1c sq-96 2022-03-03 update
html 4a5db1c sq-96 2022-03-03 update
html 75a1466 sq-96 2022-02-27 Build site.
Rmd 1c69dd2 sq-96 2022-02-27 update
html ff6403a sq-96 2022-02-27 Build site.
Rmd 3dd5b4c sq-96 2022-02-27 update

Weight QC

#number of imputed weights
nrow(qclist_all)
[1] 10567
#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 
1038  754  605  411  517  537  511  406  401  410  617  617  227  356  367  479 
  17   18   19   20   21   22 
 622  168  801  320  127  276 
#number of imputed weights without missing variants
sum(qclist_all$nmiss==0)
[1] 8626
#proportion of imputed weights without missing variants
mean(qclist_all$nmiss==0)
[1] 0.8163

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