Project info
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All commands below assume that the working directory is the NIG project folder.
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Title: Drug sensitivity prediction with normal inverse Gaussian shrinkage informed by external data
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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
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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 rpackagefor R package compilationR CMD check NIG_0.0.0.9000.tar.gzto check compiled package- installation via one of options:
install.packages("NIG_0.0.0.9000.tar.gz", repos=NULL)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 thenlibrary(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 withncores, or decreasing the number of simulation repsnrepsat 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