[R] caret package

Andrew Zhang @ndrewzh@ng20052005 @end|ng |rom gm@||@com
Sun Jul 9 08:29:54 CEST 2023

Dear all,

I am using caret package to analyze a microarray dataset with feature
selection using sbf(). My dataset is 3500 samples with 2200 genes, the
outcome Y variable is a factor of 12 levels. I used the following script to
run the feature selection:

ctrl <- sbfControl(functions=rfSBF, method='repeatedcv', repeats=5)

    ### x is a matrix of 3500x2200, y is a factor of 12 levels
obj <- sbf(x, y, sbfControl=ctrl)

But it has been more than 15 hours, the code is still running!

My computer has the following specifications:

Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz   2.00 GHz, 8 cores
16.0 GB

Does anyone know if my script has any issues, or it is normal for sbf() to
run this long?

Thank you!


> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[5] LC_TIME=English_United States.utf8

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] caret_6.0-94   lattice_0.21-8 ggplot2_3.4.2

loaded via a namespace (and not attached):
 [1] utf8_1.2.3           future_1.33.0        generics_0.1.3
 [4] class_7.3-22         stringi_1.7.12       pROC_1.18.2
 [7] listenv_0.9.0        digest_0.6.32        magrittr_2.0.3
[10] grid_4.3.1           timechange_0.2.0     iterators_1.0.14
[13] foreach_1.5.2        plyr_1.8.8           Matrix_1.5-4.1
[16] ModelMetrics_1.2.2.2 nnet_7.3-19          survival_3.5-5
[19] purrr_1.0.1          fansi_1.0.4          scales_1.2.1
[22] codetools_0.2-19     lava_1.7.2.1         cli_3.6.1
[25] rlang_1.1.1          hardhat_1.3.0        parallelly_1.36.0
[28] future.apply_1.11.0  munsell_0.5.0        splines_4.3.1
[31] withr_2.5.0          prodlim_2023.03.31   tools_4.3.1
[34] parallel_4.3.1       reshape2_1.4.4       dplyr_1.1.2
[37] colorspace_2.1-0     recipes_1.0.6        globals_0.16.2
[40] vctrs_0.6.3          R6_2.5.1             rpart_4.1.19
[43] stats4_4.3.1         lifecycle_1.0.3      lubridate_1.9.2
[46] stringr_1.5.0        MASS_7.3-60          pkgconfig_2.0.3
[49] pillar_1.9.0         gtable_0.3.3         glue_1.6.2
[52] data.table_1.14.8    Rcpp_1.0.10          tibble_3.2.1
[55] tidyselect_1.2.0     nlme_3.1-162         ipred_0.9-14
[58] timeDate_4022.108    gower_1.0.1          compiler_4.3.1

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