Question: a problem from import CTSStable in CAGEr
gravatar for Zhong JW
10 weeks ago by
Zhong JW0
Zhong JW0 wrote:

hi, I was using CAGEr whose version is 1.24.0. Before update, I can input CTSStable and analyse, but now there is some trouble here.


> input.file1 <- "G:/CAGEr/CTSS_mouse_testis_timecourse_8_samples.txt"
> samples1 <- c(paste("E", c(13,15,17), sep = ""), paste("N", c("00",10,20,30),
+                                                       sep = ""), "adult")
> myCAGEset1 <- new("CAGEset", genomeName = "BSgenome.Mmusculus.UCSC.mm9",
+                  inputFiles = input.file1, inputFilesType = "CTSStable",
+                  sampleLabels = samples1)
> getCTSS(myCAGEset1)
Error in order(...) : argument 1 is not a vector

somebody know how to solve?


> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936    LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C                               LC_TIME=Chinese (Simplified)_China.936    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggplot2_3.1.0                      BSgenome.Mmusculus.UCSC.mm10_1.4.0 BSgenome_1.50.0                   
 [4] rtracklayer_1.42.0                 Biostrings_2.50.1                  XVector_0.22.0                    
 [7] GenomicRanges_1.34.0               GenomeInfoDb_1.18.0                IRanges_2.16.0                    
[10] S4Vectors_0.20.0                   BiocGenerics_0.28.0                CAGEr_1.24.0                      

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0                  stringdist_0.9.5.1          lattice_0.20-38             formula.tools_1.7.1        
 [5] Rsamtools_1.34.0            gtools_3.8.1                assertthat_0.2.0            digest_0.6.18              
 [9] R6_2.3.0                    plyr_1.8.4                  pillar_1.3.0                zlibbioc_1.28.0            
[13] rlang_0.3.0.1               lazyeval_0.2.1              rstudioapi_0.8              data.table_1.11.8          
[17] vegan_2.5-3                 Matrix_1.2-15               splines_3.5.1               BiocParallel_1.16.0        
[21] RCurl_1.95-4.11             munsell_0.5.0               DelayedArray_0.8.0          compiler_3.5.1             
[25] pkgconfig_2.0.2             mgcv_1.8-25                 tidyselect_0.2.5            SummarizedExperiment_1.12.0
[29] tibble_1.4.2                GenomeInfoDbData_1.2.0      matrixStats_0.54.0          XML_3.98-1.16              
[33] reshape_0.8.8               permute_0.9-4               withr_2.1.2                 crayon_1.3.4               
[37] dplyr_0.7.7                 GenomicAlignments_1.18.0    MASS_7.3-51.1               bitops_1.0-6               
[41] grid_3.5.1                  nlme_3.1-137                gtable_0.2.0                magrittr_1.5               
[45] scales_1.0.0                KernSmooth_2.23-15          stringi_1.2.4               som_0.3-5.1                
[49] MultiAssayExperiment_1.8.1  bindrcpp_0.2.2              tools_3.5.1                 Biobase_2.42.0             
[53] glue_1.3.0                  purrr_0.2.5                 colorspace_1.3-2            cluster_2.0.7-1            
[57] operator.tools_1.6.3        beanplot_1.2                memoise_1.1.0               VGAM_1.0-6                 
[61] bindr_0.1.1            


cager • 66 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Zhong JW0

Hi, can you send me some sample data, by email or by opening an issue on GitHub ?

ADD REPLYlink written 5 weeks ago by Charles Plessy90
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