https://github.com/bhklab/cdrug-rebuttal
Code for "Assessment of pharmacogenomic agreement" by Safikhani et al -> Response to "Pharmacogenomic agreement between two cancer cell line data sets" by the GDSC/CCLE investigators
https://github.com/bhklab/cdrug-rebuttal
analysis
Last synced: 4 months ago
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Code for "Assessment of pharmacogenomic agreement" by Safikhani et al -> Response to "Pharmacogenomic agreement between two cancer cell line data sets" by the GDSC/CCLE investigators
- Host: GitHub
- URL: https://github.com/bhklab/cdrug-rebuttal
- Owner: bhklab
- Created: 2016-04-27T21:43:48.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2016-04-27T21:46:56.000Z (about 9 years ago)
- Last Synced: 2024-12-30T03:24:22.044Z (6 months ago)
- Topics: analysis
- Language: R
- Size: 7.81 KB
- Stars: 0
- Watchers: 4
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.txt
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README
README file for: Assessment of pharmacogenomic agreement
Zhaleh Safikhani, Nehme El-Hachem, Rene Quevedo, Petr Smirnov, Anna Goldenberg, Nicolai Juul Birkbak, Christopher Mason, Christos Hatzis, Leming Shi, Hugo JWL Aerts, John Quackenbush, Benjamin Haibe-Kains
1. Copy Data_File_1.R and Data_File_2.csv in one directory
2. Open an R session and set the directory to the one containing Data Files.
3. Run Data_File_1.R
4. Note that it requires installation of PharmcoGx package which is coded in the R file and your R session should be as following after loading PharmacoGx package into your R session:
sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biobase_2.30.0 BiocGenerics_0.16.1 PharmacoGx_1.1.4 BiocInstaller_1.20.1
loaded via a namespace (and not attached):
[1] mclust_5.1 Rcpp_0.12.3 lattice_0.20-33 relations_0.6-6
[5] class_7.3-13 piano_1.10.2 gtools_3.5.0 digest_0.6.9
[9] slam_0.1-32 plyr_1.8.3 acepack_1.3-3.3 stats4_3.2.2
[13] RSQLite_1.0.0 e1071_1.6-7 ggplot2_2.1.0 gplots_2.17.0
[17] iC10_1.1.3 gdata_2.17.0 S4Vectors_0.8.3 rpart_4.1-10
[21] magicaxis_1.9.4 splines_3.2.2 sets_1.0-16 epibasix_1.3
[25] genefu_2.2.0 downloader_0.4 foreign_0.8-65 igraph_1.0.1
[29] RCurl_1.95-4.7 biomaRt_2.26.1 munsell_0.4.3 survcomp_1.20.0
[33] marray_1.48.0 AIMS_1.2.0 nnet_7.3-10 gridExtra_2.2.1
[37] prodlim_1.5.5 Hmisc_3.17-2 IRanges_2.4.4 XML_3.98-1.3
[41] MASS_7.3-43 bitops_1.0-6 SuppDists_1.1-9.1 grid_3.2.2
[45] gtable_0.2.0 DBI_0.3.1 magrittr_1.5 scales_0.4.0
[49] KernSmooth_2.23-15 amap_0.8-14 iC10TrainingData_1.0.1 sm_2.2-5.4
[53] limma_3.26.3 latticeExtra_0.6-28 Formula_1.2-1 rmeta_2.16
[57] lava_1.4.1 RColorBrewer_1.1-2 tools_3.2.2 pamr_1.55
[61] plotrix_3.6-1 survival_2.38-3 AnnotationDbi_1.32.0 colorspace_1.2-6
[65] cluster_2.0.3 caTools_1.17.1 survivalROC_1.0.3 bootstrap_2015.2