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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
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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
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