options(stringsAsFactors = FALSE) breaks TRONCO

[rdiaz02]

The second call to tronco.caprese fails, with a very confusing message from bnlearn:

library(TRONCO)

x <- data.frame(A = c(1, 1, 1, 0, 0),
                B = c(0, 0, 1, 0, 1))
tronco.caprese(import.genotypes(x))

options(stringsAsFactors = FALSE)

tronco.caprese(import.genotypes(x))

Note that the problem does not seem to be in the call to import.genotypes.

Output from sessionInfo()

> sessionInfo()
R version 3.3.0 Patched (2016-05-26 r70677)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] TRONCO_2.4.2

loaded via a namespace (and not attached):
 [1] igraph_1.0.1         graph_1.50.0         Rcpp_0.12.5         
 [4] magrittr_1.5         BiocGenerics_0.18.0  gRapHD_0.2.4        
 [7] munsell_0.4.3        doParallel_1.0.10    xtable_1.8-2        
[10] colorspace_1.2-6     foreach_1.4.3        plyr_1.8.3          
[13] parallel_3.3.0       grid_3.3.0           gtable_0.2.0        
[16] circlize_0.3.7       R.oo_1.20.0          R.matlab_3.5.1      
[19] iterators_1.0.8      infotheo_1.2.0       gridExtra_2.2.1     
[22] RColorBrewer_1.1-2   Rgraphviz_2.16.0     cgdsr_1.2.5         
[25] R.utils_2.3.0        GlobalOptions_0.0.10 codetools_0.2-14    
[28] shape_1.4.2          scales_0.4.0         R.methodsS3_1.7.1   
[31] stats4_3.3.0         bnlearn_4.0         
> 

[luca-dex]

@rdiaz02 thank you for your work. Please let me know if the issue you reported is solved