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 rpackage
for R package compilationR CMD check NIG_0.0.0.9000.tar.gz
to 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"))
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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 repsnreps
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