magnusmunch/NIG

Project info

All commands below assume that the working directory is the NIG project folder.
Title: Drug sensitivity prediction with normal inverse Gaussian shrinkage informed by external data
Authors: Magnus M. Münch (responsible for writing code, email: m.munch@amsterdamumc.nl), Mark A. van de Wiel, Sylvia Richardson, and Gwenaël G. R. Leday
configuration:

─ Session info ──────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.3 (2020-02-29)
 os       macOS Catalina 10.15.3      
 system   x86_64, darwin15.6.0        
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Brussels             
 date     2020-04-28                  

─ Packages ──────────────────────────────────────────────────────────────────────────────
 package       * version    date       lib source        
 AnnotationDbi   1.48.0     2019-10-29 [1] Bioconductor  
 askpass         1.1        2019-01-13 [1] CRAN (R 3.6.0)
 assertthat      0.2.1      2019-03-21 [1] CRAN (R 3.6.0)
 backports       1.1.6      2020-04-05 [1] CRAN (R 3.6.2)
 Biobase         2.46.0     2019-10-29 [1] Bioconductor  
 BiocFileCache   1.10.2     2019-11-08 [1] Bioconductor  
 BiocGenerics    0.32.0     2019-10-29 [1] Bioconductor  
 biomaRt       * 2.42.1     2020-03-26 [1] Bioconductor  
 bit             1.1-15.2   2020-02-10 [1] CRAN (R 3.6.0)
 bit64           0.9-7      2017-05-08 [1] CRAN (R 3.6.0)
 blob            1.2.1      2020-01-20 [1] CRAN (R 3.6.0)
 callr           3.4.3      2020-03-28 [1] CRAN (R 3.6.2)
 cli             2.0.2      2020-02-28 [1] CRAN (R 3.6.0)
 codetools       0.2-16     2018-12-24 [1] CRAN (R 3.6.3)
 colorspace      1.4-1      2019-03-18 [1] CRAN (R 3.6.0)
 crayon          1.3.4      2017-09-16 [1] CRAN (R 3.6.0)
 curl            4.3        2019-12-02 [1] CRAN (R 3.6.0)
 DBI             1.1.0      2019-12-15 [1] CRAN (R 3.6.0)
 dbplyr          1.4.2      2019-06-17 [1] CRAN (R 3.6.0)
 desc            1.2.0      2018-05-01 [1] CRAN (R 3.6.0)
 devtools        2.3.0      2020-04-10 [1] CRAN (R 3.6.3)
 digest          0.6.25     2020-02-23 [1] CRAN (R 3.6.0)
 doParallel    * 1.0.15     2019-08-02 [1] CRAN (R 3.6.0)
 dplyr           0.8.5      2020-03-07 [1] CRAN (R 3.6.0)
 ellipsis        0.3.0      2019-09-20 [1] CRAN (R 3.6.0)
 fansi           0.4.1      2020-01-08 [1] CRAN (R 3.6.0)
 foreach       * 1.5.0      2020-03-30 [1] CRAN (R 3.6.2)
 fs              1.4.1      2020-04-04 [1] CRAN (R 3.6.2)
 gdata         * 2.18.0     2017-06-06 [1] CRAN (R 3.6.0)
 ggplot2       * 3.3.0      2020-03-05 [1] CRAN (R 3.6.0)
 glmnet        * 3.0-2      2019-12-11 [1] CRAN (R 3.6.0)
 glue            1.4.0      2020-04-03 [1] CRAN (R 3.6.2)
 gridExtra       2.3        2017-09-09 [1] CRAN (R 3.6.0)
 gsl             2.1-6      2019-03-25 [1] CRAN (R 3.6.3)
 gtable          0.3.0      2019-03-25 [1] CRAN (R 3.6.0)
 gtools          3.8.2      2020-03-31 [1] CRAN (R 3.6.2)
 hms             0.5.3      2020-01-08 [1] CRAN (R 3.6.0)
 httr            1.4.1      2019-08-05 [1] CRAN (R 3.6.0)
 inline          0.3.15     2018-05-18 [1] CRAN (R 3.6.0)
 IRanges         2.20.2     2020-01-13 [1] Bioconductor  
 iterators     * 1.0.12     2019-07-26 [1] CRAN (R 3.6.0)
 lattice         0.20-38    2018-11-04 [1] CRAN (R 3.6.3)
 lifecycle       0.2.0      2020-03-06 [1] CRAN (R 3.6.0)
 loo             2.2.0      2019-12-19 [1] CRAN (R 3.6.0)
 magrittr        1.5        2014-11-22 [1] CRAN (R 3.6.0)
 Matrix        * 1.2-18     2019-11-27 [1] CRAN (R 3.6.3)
 matrixStats     0.56.0     2020-03-13 [1] CRAN (R 3.6.0)
 memoise         1.1.0      2017-04-21 [1] CRAN (R 3.6.0)
 munsell         0.5.0      2018-06-12 [1] CRAN (R 3.6.0)
 NIG           * 0.0.0.9000 2020-04-21 [1] local         
 openssl         1.4.1      2019-07-18 [1] CRAN (R 3.6.0)
 pillar          1.4.3      2019-12-20 [1] CRAN (R 3.6.0)
 pkgbuild        1.0.6      2019-10-09 [1] CRAN (R 3.6.0)
 pkgconfig       2.0.3      2019-09-22 [1] CRAN (R 3.6.0)
 pkgload         1.0.2      2018-10-29 [1] CRAN (R 3.6.0)
 prettyunits     1.1.1      2020-01-24 [1] CRAN (R 3.6.0)
 processx        3.4.2      2020-02-09 [1] CRAN (R 3.6.0)
 progress        1.2.2      2019-05-16 [1] CRAN (R 3.6.0)
 ps              1.3.2      2020-02-13 [1] CRAN (R 3.6.0)
 purrr           0.3.3      2019-10-18 [1] CRAN (R 3.6.0)
 R6              2.4.1      2019-11-12 [1] CRAN (R 3.6.0)
 rappdirs        0.3.1      2016-03-28 [1] CRAN (R 3.6.0)
 Rcpp            1.0.4.6    2020-04-09 [1] CRAN (R 3.6.3)
 remotes         2.1.1      2020-02-15 [1] CRAN (R 3.6.0)
 rlang           0.4.5      2020-03-01 [1] CRAN (R 3.6.0)
 rprojroot       1.3-2      2018-01-03 [1] CRAN (R 3.6.0)
 RSQLite         2.2.0      2020-01-07 [1] CRAN (R 3.6.0)
 rstan         * 2.19.3     2020-02-11 [1] CRAN (R 3.6.0)
 rstudioapi      0.11       2020-02-07 [1] CRAN (R 3.6.0)
 S4Vectors       0.24.4     2020-04-09 [1] Bioconductor  
 scales          1.1.0      2019-11-18 [1] CRAN (R 3.6.0)
 sessioninfo     1.1.1      2018-11-05 [1] CRAN (R 3.6.0)
 shape           1.4.4      2018-02-07 [1] CRAN (R 3.6.0)
 StanHeaders   * 2.21.0-1   2020-01-19 [1] CRAN (R 3.6.0)
 statmod       * 1.4.34     2020-02-17 [1] CRAN (R 3.6.0)
 stringi         1.4.6      2020-02-17 [1] CRAN (R 3.6.0)
 stringr         1.4.0      2019-02-10 [1] CRAN (R 3.6.0)
 testthat        2.3.2      2020-03-02 [1] CRAN (R 3.6.0)
 tibble          3.0.0      2020-03-30 [1] CRAN (R 3.6.2)
 tidyselect      1.0.0      2020-01-27 [1] CRAN (R 3.6.0)
 usethis         1.6.0      2020-04-09 [1] CRAN (R 3.6.3)
 vctrs           0.2.4      2020-03-10 [1] CRAN (R 3.6.0)
 withr           2.1.2      2018-03-15 [1] CRAN (R 3.6.0)
 XML             3.99-0.3   2020-01-20 [1] CRAN (R 3.6.0)
 yaml            2.2.1      2020-02-01 [1] CRAN (R 3.6.0)

packages

required R packages, available from CRAN:

knitr
kableExtra
gdata
sp
GeneralizedHyperbolic

available from bioconductor:

biomaRt

install R package

R CMD build rpackage for R package compilation
R CMD check NIG_0.0.0.9000.tar.gz to check compiled package
installation via one of options:
1. install.packages("NIG_0.0.0.9000.tar.gz", repos=NULL)
2. library(devtools); install_github("magnusmunch/NIG/rpackage", local=FALSE, auth_token="yourtoken"), where "yourtoken" is exchanged with a personal Github token, created with Settings > Developer settings > Personal access tokens. Alternatively, one (1) creates a personal token on Github as explained before, (2) copies the token and (3) adds the following line to the environment settings in .Rprofile: Sys.setenv(GITHUB_PAT="yourtoken"), where "yourtoken" is exchanged with the copied token. (4) Installation is then library(devtools); install_github("magnusmunch/NIG/code", local=FALSE, auth_token=Sys.getenv("GITHUB_PAT")).

Results

R code files are in code folder
data preparation scripts are in code/data_ccle.R and code/data_gdsc.R
GDSC data based simulations are in code/simulations_gdsc.R
data analysis scripts are in code/analysis_ccle.R and code/analysis_gdsc.R
figure creation script is code/figures.R
to generate the results, run the code in code/all_results.R. This may take a few days. To speed up, consider lowering the number of cross validation folds nfolds, increasing the number of cores to compute with ncores, or decreasing the number of simulation reps nreps at the top of the file.

Manuscript

compile docs/manuscript.rnw for manuscript (e.g., in R studio using knitr)
compile docs/supplement.rnw for supplementary material (e.g., in R studio using knitr)
citation style is in docs/author_short3.bst file
bib references are in docs/refs.bib

Data

CCLE data retrieved from: https://portals.broadinstitute.org/ccle
GDSC data retrieved from: https://www.cancerrxgene.org

magnusmunch / NIG

Project info

packages

install R package

Results

Manuscript

Data

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