Last updated: 2017-07-18

Code version: 49915de

Here ,we presents more examples of dimer from the database from atSNP package. The database only contains position probability matrix(from directly scaling of pfm) and the number of counts at each position is unkown. So the findings based on these data may be unreliable. Despite this, we found some TF families that have tipical dimer characteristics.

EBF1 family: G depleted followed by C. (CG); dimer, with depletion in the middle.

for(i in grep('EBF1',names(PWMencode))){
  nlogomaker(PWMencode[[i]],logoheight = 'ic',color_profile = color_profile,frame_width = 1,ylimit=2.1,pop_name = names(PWMencode[i]))
}

TFAP2 family: dimer, with depletion in the middle.

for(i in grep('TFAP2',names(PWMencode))){
  nlogomaker(PWMencode[[i]],logoheight = 'ic',color_profile = color_profile,frame_width = 1,ylimit=2.1,pop_name = names(PWMencode[i]))
}

Session information

sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] Logolas_1.1.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11       digest_0.6.12      rprojroot_1.2     
 [4] grid_3.4.0         backports_1.0.5    git2r_0.18.0      
 [7] magrittr_1.5       evaluate_0.10      stringi_1.1.5     
[10] rmarkdown_1.6      RColorBrewer_1.1-2 tools_3.4.0       
[13] stringr_1.2.0      yaml_2.1.14        compiler_3.4.0    
[16] htmltools_0.3.5    knitr_1.15.1

This R Markdown site was created with workflowr