FLASH on chrommarks_chipcounts_example_regions

Last updated: 2017-02-13

Code version: d8519d7

#GM12878 = readRDS("~/HG/flash_workflow/data/chrommarks_chipcounts_example_regions/GM12878_10marks_meanChIP_chr1_region_asinh.rds")
#Y = GM12878[,1:9]
#g_flash = flashr::greedy(Y, K = 8, flash_para = list(partype = "var_col"))
#b_flash = flashr::backfitting(Y,initial_list = g_flash, flash_para = list(partype = "var_col"), maxiter_bf = 10)
#FL_GM = b_flash
#saveRDS(FL_GM, "~/HG/flash_workflow/data/chrommarks_chipcounts_example_regions/FL_GM_var_col.rds")
FL_GM = readRDS("~/HG/flash_workflow/data/chrommarks_chipcounts_example_regions/FL_GM_var_col.rds")

HUVEC = readRDS("~/HG/flash_workflow/data/chrommarks_chipcounts_example_regions/HUVEC_10marks_meanChIP_chr1_region_asinh.rds")
#Y = HUVEC[,1:9]
#g_flash = flashr::greedy(Y, K = 8, flash_para = list(partype = "var_col"))
#b_flash = flashr::backfitting(Y,initial_list = g_flash, flash_para = list(partype = "var_col"), maxiter_bf = 10)
#FL_HUVEC = b_flash
#saveRDS(FL_HUVEC, "~/HG/flash_workflow/data/chrommarks_chipcounts_example_regions/FL_HUVEC_var_col.rds")

#K562 = readRDS("~/HG/flash_workflow/data/chrommarks_chipcounts_example_regions/K562_10marks_meanChIP_chr1_region_asinh.rds")
#Y = K562[,1:9]
#g_flash = flashr::greedy(Y, K = 8, flash_para = list(partype = "var_col"))
#b_flash = flashr::backfitting(Y,initial_list = g_flash, flash_para = list(partype = "var_col"), maxiter_bf = 10)
#FL_K562 = b_flash
#saveRDS(FL_K562, "~/HG/flash_workflow/data/chrommarks_chipcounts_example_regions/FL_K562_var_col.rds")
FL_K562 = readRDS("~/HG/flash_workflow/data/chrommarks_chipcounts_example_regions/FL_K562_var_col.rds")

#NHLF = readRDS("~/HG/flash_workflow/data/chrommarks_chipcounts_example_regions/NHLF_10marks_meanChIP_chr1_region_asinh.rds")
#Y = NHLF[,1:9]
#g_flash = flashr::greedy(Y, K = 8, flash_para = list(partype = "var_col"))
#b_flash = flashr::backfitting(Y,initial_list = g_flash, flash_para = list(partype = "var_col"), maxiter_bf = 10)
#FL_NHLF = b_flash
#saveRDS(FL_NHLF, "~/HG/flash_workflow/data/chrommarks_chipcounts_example_regions/FL_NHLF_var_col.rds")
FL_NHLF = readRDS("~/HG/flash_workflow/data/chrommarks_chipcounts_example_regions/FL_NHLF_var_col.rds")

sessionInfo()

R version 3.2.4 (2016-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.3 (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] flashr_0.1.1    workflowr_0.3.0 rmarkdown_1.3  

loaded via a namespace (and not attached):
 [1] igraph_1.0.1      Rcpp_0.12.7       rstudioapi_0.6   
 [4] knitr_1.15.1      magrittr_1.5      REBayes_0.63     
 [7] MASS_7.3-45       doParallel_1.0.10 pscl_1.4.9       
[10] SQUAREM_2016.8-2  lattice_0.20-34   foreach_1.4.3    
[13] ashr_2.0.3        stringr_1.1.0     tools_3.2.4      
[16] parallel_3.2.4    grid_3.2.4        irlba_2.1.2      
[19] git2r_0.18.0      htmltools_0.3.5   iterators_1.0.8  
[22] assertthat_0.1    yaml_2.1.14       rprojroot_1.2    
[25] digest_0.6.11     Matrix_1.2-7.1    codetools_0.2-15 
[28] rsconnect_0.4.3   evaluate_0.10     stringi_1.1.2    
[31] Rmosek_7.1.2      backports_1.0.5   flare_1.5.0      
[34] truncnorm_1.0-7  

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