Search
Question: a problem from import CTSStable in CAGEr
0
gravatar for Zhong JW
12 days 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

locale:
[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            

 

ADD COMMENTlink modified 12 days ago • written 12 days ago by Zhong JW0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 403 users visited in the last hour