GoM clustering of genome locations using chromatin marks

load data

cell types: K562 GM12878 HUVEC NHLF 

Data dimension: 18000 rows x 10 columns 

53.1 % zeros in the matrix

GoM clustering

Estimating on a 17548 document collection.
Fitting the 2 topic model.
log posterior increase: 16392.4, done.
          topic
phrase        1    2
  CTCF     0.18 0.02
  H3K27me3 0.22 0.00
  H3K36me3 0.15 0.02
  H4K20me1 0.15 0.01
  H3K4me1  0.03 0.23
  H3K4me2  0.01 0.18
  H3K4me3  0.09 0.15
  H3K27ac  0.00 0.22
  H3K9ac   0.03 0.13
  Control  0.14 0.02

Structure plot 

Estimating on a 17548 document collection.
Fitting the 3 topic model.
log posterior increase: 19709.7, done.
          topic
phrase        1    2    3
  CTCF     0.01 0.00 0.33
  H3K27me3 0.32 0.00 0.01
  H3K36me3 0.19 0.02 0.05
  H4K20me1 0.22 0.01 0.01
  H3K4me1  0.02 0.31 0.01
  H3K4me2  0.00 0.23 0.02
  H3K4me3  0.02 0.04 0.39
  H3K27ac  0.00 0.28 0.01
  H3K9ac   0.01 0.10 0.16
  Control  0.22 0.02 0.01

Structure plot 

Estimating on a 17548 document collection.
Fitting the 4 topic model.
log posterior increase: 22759.3, done.
          topic
phrase        1    2    3    4
  CTCF     0.00 0.00 0.00 0.78
  H3K27me3 0.38 0.00 0.00 0.04
  H3K36me3 0.08 0.01 0.19 0.05
  H4K20me1 0.26 0.01 0.01 0.02
  H3K4me1  0.01 0.35 0.00 0.03
  H3K4me2  0.00 0.24 0.05 0.00
  H3K4me3  0.01 0.02 0.44 0.04
  H3K27ac  0.00 0.29 0.06 0.00
  H3K9ac   0.00 0.07 0.25 0.01
  Control  0.25 0.02 0.01 0.03

Structure plot 

Estimating on a 17548 document collection.
Fitting the 5 topic model.
log posterior increase: 20147, 290.3, done.
          topic
phrase        1    2    3    4    5
  CTCF     0.00 0.00 0.00 0.00 0.89
  H3K27me3 0.47 0.00 0.00 0.00 0.02
  H3K36me3 0.00 0.00 0.00 0.66 0.00
  H4K20me1 0.26 0.01 0.00 0.12 0.01
  H3K4me1  0.00 0.39 0.00 0.05 0.01
  H3K4me2  0.00 0.24 0.10 0.00 0.00
  H3K4me3  0.01 0.00 0.49 0.02 0.04
  H3K27ac  0.00 0.29 0.11 0.00 0.00
  H3K9ac   0.00 0.04 0.30 0.01 0.00
  Control  0.25 0.02 0.00 0.13 0.02

Structure plot 

Estimating on a 17548 document collection.
Fitting the 6 topic model.
log posterior increase: 17296.4, 574.9, done.
          topic
phrase        1    2    3    4    5    6
  CTCF     0.00 0.00 0.00 0.00 0.00 0.94
  H3K27me3 0.67 0.00 0.00 0.00 0.00 0.01
  H3K36me3 0.00 0.00 0.00 0.72 0.00 0.00
  H4K20me1 0.32 0.01 0.00 0.20 0.01 0.01
  H3K4me1  0.00 0.39 0.00 0.05 0.05 0.01
  H3K4me2  0.00 0.25 0.10 0.00 0.00 0.00
  H3K4me3  0.00 0.00 0.51 0.01 0.01 0.03
  H3K27ac  0.00 0.30 0.10 0.00 0.00 0.00
  H3K9ac   0.00 0.05 0.28 0.01 0.07 0.00
  Control  0.00 0.00 0.00 0.00 0.85 0.00

Structure plot 

Estimating on a 17548 document collection.
Fitting the 7 topic model.
log posterior increase: 18079.9, 464.2, 332.9, done.
          topic
phrase        1    2    3    4    5    6 7
  CTCF     0.00 0.00 0.00 0.00 0.00 0.00 1
  H3K27me3 0.61 0.00 0.00 0.02 0.00 0.00 0
  H3K36me3 0.00 0.00 0.00 0.00 0.00 0.90 0
  H4K20me1 0.39 0.01 0.01 0.00 0.00 0.09 0
  H3K4me1  0.00 0.59 0.00 0.00 0.00 0.01 0
  H3K4me2  0.00 0.28 0.17 0.00 0.00 0.00 0
  H3K4me3  0.00 0.00 0.04 0.98 0.00 0.00 0
  H3K27ac  0.00 0.12 0.42 0.00 0.00 0.00 0
  H3K9ac   0.00 0.00 0.37 0.00 0.05 0.00 0
  Control  0.00 0.00 0.00 0.00 0.94 0.00 0

Structure plot 

Session Information

sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

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] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] flashr_0.1.1       workflowr_0.3.0    rmarkdown_1.3     
 [4] RColorBrewer_1.1-2 randomcoloR_1.0.0  gridExtra_2.2.1   
 [7] maptpx_1.9-2       slam_0.1-40        CountClust_0.1.2  
[10] ggplot2_2.2.1      gplots_3.0.1      

loaded via a namespace (and not attached):
 [1] gtools_3.5.0       modeltools_0.2-21  reshape2_1.4.2    
 [4] ashr_2.1.5         lattice_0.20-34    V8_1.2            
 [7] colorspace_1.3-2   htmltools_0.3.5    stats4_3.3.2      
[10] yaml_2.1.14        mgcv_1.8-16        foreach_1.4.3     
[13] plyr_1.8.4         stringr_1.2.0      munsell_0.4.3     
[16] gtable_0.2.0       caTools_1.17.1     codetools_0.2-15  
[19] evaluate_0.10      knitr_1.15.1       permute_0.9-4     
[22] pscl_1.4.9         doParallel_1.0.10  flexmix_2.3-13    
[25] parallel_3.3.2     curl_2.3           Rcpp_0.12.9       
[28] KernSmooth_2.23-15 scales_0.4.1       backports_1.0.5   
[31] limma_3.28.21      gdata_2.17.0       vegan_2.4-2       
[34] jsonlite_1.2       truncnorm_1.0-7    picante_1.6-2     
[37] digest_0.6.12      stringi_1.1.2      cowplot_0.7.0     
[40] rprojroot_1.2      tools_3.3.2        bitops_1.0-6      
[43] magrittr_1.5       lazyeval_0.2.0     tibble_1.2        
[46] cluster_2.0.5      ape_4.0            MASS_7.3-45       
[49] Matrix_1.2-8       SQUAREM_2016.8-2   rsconnect_0.7     
[52] iterators_1.0.8    assertthat_0.1     nnet_7.3-12       
[55] nlme_3.1-130       git2r_0.18.0