Last updated: 2018-02-11
Code version: d53227e
To reproduce our results on your own computer, please follow these setup instructions.
install.packages(c("devtools", "ashr", "PMA","ssvd","softImpute","Matrix","R.matlab","ggplot2","denoiseR"))
devtools::install_github("stephenslab/flashr")All the data sets used in the paper are in data files
Here are details about the computing environment, including the version of R and the R packages, that were used to generate the results from the R Markdown documents.
sessionInfo()R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.13.3 (unknown)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] denoiseR_1.0 scales_0.4.1 MASS_7.3-47 reshape2_1.4.3
[5] flashr_0.4-6 workflowr_0.4.0 rmarkdown_1.6 ggplot2_2.2.1
[9] R.matlab_3.6.1 softImpute_1.4 Matrix_1.2-11 PMA_1.0.9
[13] impute_1.48.0 plyr_1.8.4 ssvd_1.0
loaded via a namespace (and not attached):
[1] ashr_2.2-3 lattice_0.20-35 colorspace_1.3-2
[4] htmltools_0.3.6 yaml_2.1.16 rlang_0.1.6
[7] R.oo_1.21.0 withr_2.1.1 R.utils_2.5.0
[10] foreach_1.4.4 stringr_1.2.0 munsell_0.4.3
[13] gtable_0.2.0 R.methodsS3_1.7.1 devtools_1.13.3
[16] codetools_0.2-15 leaps_3.0 evaluate_0.10.1
[19] memoise_1.1.0 labeling_0.3 knitr_1.18
[22] pscl_1.5.2 doParallel_1.0.11 irlba_2.2.1
[25] parallel_3.3.0 curl_2.8.1 Rcpp_0.12.14
[28] flashClust_1.01-2 backports_1.1.2 scatterplot3d_0.3-40
[31] truncnorm_1.0-7 gridExtra_2.3 digest_0.6.13
[34] stringi_1.1.6 flashr2_0.4-0 grid_3.3.0
[37] rprojroot_1.2 tools_3.3.0 magrittr_1.5
[40] lazyeval_0.2.0 tibble_1.3.4 cluster_2.0.6
[43] FactoMineR_1.36 SQUAREM_2017.10-1 httr_1.3.0
[46] rstudioapi_0.6 iterators_1.0.9 R6_2.2.2
[49] git2r_0.19.0 This R Markdown site was created with workflowr