Error run cghMCR function in cghMCR package
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ljia1180 • 0
Last seen 3.9 years ago

Dear Users,

I run into an error message when running cghMCR function using cghMCR package.

>cghmcr <- cghMCR(segDat, gapAllowed = 500, alteredLow = 0.2, alteredHigh = 0.8, recurrence = 50)

> cghmcr
Object of cghMCR
    Row = 31
    Column = 6
Error in cat(DNASeg(object)[1:rows, ]) :
  argument 1 (type 'list') cannot be handled by 'cat'


I tried both ways, one used the object generated from DNAcopy segment, it doesn't work. I tried the way to generate a list using data, output and call that are similar to segment object. Unfortunately both ways gave the same error message as above. I didn't see DNASeg used in the package, i have no idea where this information comes from.

I also updated the version to 1.36, please see below

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

[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] tools     grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] edgeR_3.20.1      reshape_0.8.7     cghMCR_1.36.0     CNTools_1.26.0    genefilter_1.52.1 DNAcopy_1.44.0   
 [7] limma_3.26.9      xlsx_0.5.7        xlsxjars_0.6.1    rJava_0.9-9       expands_2.0.0     ggplot2_2.2.1    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13         compiler_3.4.2       plyr_1.8.4           moments_0.14         digest_0.6.12       
 [6] bit_1.1-12           annotate_1.48.0      RSQLite_2.0          memoise_1.1.0        tibble_1.3.4        
[11] nlme_3.1-131         gtable_0.2.0         lattice_0.20-35      rlang_0.1.2          Matrix_1.2-11       
[16] DBI_0.7              yaml_2.1.14          parallel_3.4.2       IRanges_2.12.0       S4Vectors_0.16.0    
[21] locfit_1.5-9.1       stats4_3.4.2         bit64_0.9-7          nnet_7.3-12          Biobase_2.30.0      
[26] flexmix_2.3-14       AnnotationDbi_1.32.3 survival_2.41-3      XML_3.98-1.9         matlab_1.0.2        
[31] blob_1.1.0           splines_3.4.2        scales_0.5.0         modeltools_0.2-21    BiocGenerics_0.24.0
[36] ape_5.0              colorspace_1.3-2     xtable_1.8-2         labeling_0.3         lazyeval_0.2.1      
[41] munsell_0.4.3   

Thanks for the help! really appreciate it.



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