Last updated: 2018-10-11

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  • ✔ R Markdown file: up-to-date

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  • ✔ Environment: empty

    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.

  • ✔ Seed: set.seed(20180719)

    The command set.seed(20180719) 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.

  • ✔ Session information: recorded

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  • ✔ Repository version: b7c4d09

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    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
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Expand here to see past versions:
    File Version Author Date Message
    Rmd b7c4d09 Xiang Zhu 2018-10-11 wflow_publish(“analysis/wtccc_fulldata_liver.Rmd”)
    html cc6b9f4 Xiang Zhu 2018-09-24 Build site.
    Rmd 09af305 Xiang Zhu 2018-09-24 wflow_publish(“analysis/wtccc_fulldata_liver.Rmd”)
    html e083aa6 Xiang Zhu 2018-09-20 Build site.
    Rmd f31ab76 Xiang Zhu 2018-09-20 wflow_publish(“analysis/wtccc_fulldata_liver.Rmd”)

PIP: 0.1 & PVE: 0.2

True total number of genes with nonzero effect:  1804 
Estimated total number of genes with nonzero effect:  1812.836 
True PVE:  0.2 
Estimated PVE: 0.2028945

Expand here to see past versions of unnamed-chunk-3-1.png:
Version Author Date
cc6b9f4 Xiang Zhu 2018-09-24
e083aa6 Xiang Zhu 2018-09-20

PIP: 0.2 & PVE: 0.2

True total number of genes with nonzero effect:  3640 
Estimated total number of genes with nonzero effect:  3647.185 
True PVE:  0.2 
Estimated PVE: 0.1916802

Expand here to see past versions of unnamed-chunk-4-1.png:
Version Author Date
cc6b9f4 Xiang Zhu 2018-09-24
e083aa6 Xiang Zhu 2018-09-20

PIP: 0.2 & PVE: 0.4

True total number of genes with nonzero effect:  3640 
Estimated total number of genes with nonzero effect:  3613.789 
True PVE:  0.4 
Estimated PVE: 0.4048478

Expand here to see past versions of unnamed-chunk-5-1.png:
Version Author Date
cc6b9f4 Xiang Zhu 2018-09-24
e083aa6 Xiang Zhu 2018-09-20

Session information

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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     

other attached packages:
[1] bindrcpp_0.2.2 plotROC_2.2.1  ggpubr_0.1.8   magrittr_1.5  
[5] ggplot2_3.0.0  R.matlab_3.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.19      compiler_3.5.1    pillar_1.3.0     
 [4] git2r_0.23.0      plyr_1.8.4        workflowr_1.1.1  
 [7] bindr_0.1.1       R.methodsS3_1.7.1 R.utils_2.7.0    
[10] tools_3.5.1       digest_0.6.17     evaluate_0.11    
[13] tibble_1.4.2      gtable_0.2.0      pkgconfig_2.0.2  
[16] rlang_0.2.2       yaml_2.2.0        withr_2.1.2      
[19] stringr_1.3.1     dplyr_0.7.6       knitr_1.20       
[22] cowplot_0.9.3     rprojroot_1.3-2   grid_3.5.1       
[25] tidyselect_0.2.4  data.table_1.11.8 glue_1.3.0       
[28] R6_2.3.0          rmarkdown_1.10    purrr_0.2.5      
[31] whisker_0.3-2     backports_1.1.2   scales_1.0.0     
[34] htmltools_0.3.6   assertthat_0.2.0  colorspace_1.3-2 
[37] labeling_0.3      stringi_1.2.4     lazyeval_0.2.1   
[40] munsell_0.5.0     crayon_1.3.4      R.oo_1.22.0

This reproducible R Markdown analysis was created with workflowr 1.1.1