Hi,

I'm trying to use this program to analyze four human (aligned to hg19) 4C-Seq samples - two experimental conditions with two replicates each. I'm following the vignette workflow. After adjusting the minCount (= 300) and minDist (=14000) parameters in getZScores, I've ended up with nice-looking normal q-q plots, and the plotFits plots for all four samples show the expected interactions between my viewpoint enhancer and fragments at the target promoter and an adjacent enhancer.

However, I can't get plotZScores to work at all - I keep getting the following cryptic error:

> plotZScores(fcf1[,c("viewpoint1_DMSO_1", "viewpoint1_DMSO_2")], plotWindows = c(5e+04, 5e+06),
+ txdb=TxDb.Hsapiens.UCSC.hg19.knownGene)
[1] "viewpoint1"
Error in combine_vars(data, params$plot_env, cols, drop = params$drop) :
  At least one layer must contain all variables used for facetting
In addition: Warning messages:
1: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
2: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
3: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

Does anyone know what's going on? I've tried to run this without the txdb argument, but then I just get this error:

Error: Objects of type standardGeneric not supported by autoplot.

Any help much appreciated!

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.5 (Sierra)

locale:
[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] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.24.5                 
 [3] AnnotationDbi_1.34.4                    FourCSeq_1.6.2                         
 [5] LSD_3.0                                 DESeq2_1.12.4                          
 [7] SummarizedExperiment_1.2.3              Biobase_2.32.0                         
 [9] ggplot2_2.2.1                           GenomicRanges_1.24.3                   
[11] GenomeInfoDb_1.8.7                      IRanges_2.6.1                          
[13] S4Vectors_0.10.3                        BiocGenerics_0.18.0                    
[15] BiocInstaller_1.22.3                   

loaded via a namespace (and not attached):
 [1] httr_1.2.1                    AnnotationHub_2.4.2           bit64_0.9-7                  
 [4] gtools_3.5.0                  shiny_1.0.3                   Formula_1.2-1                
 [7] interactiveDisplayBase_1.10.3 latticeExtra_0.6-28           RBGL_1.48.1                  
[10] blob_1.1.0                    BSgenome_1.40.1               Rsamtools_1.24.0             
[13] RSQLite_2.0                   backports_1.1.0               lattice_0.20-35              
[16] biovizBase_1.20.0             digest_0.6.12                 RColorBrewer_1.1-2           
[19] XVector_0.12.1                checkmate_1.8.3               colorspace_1.3-2             
[22] ggbio_1.20.2                  httpuv_1.3.5                  htmltools_0.3.6              
[25] Matrix_1.2-10                 plyr_1.8.4                    OrganismDbi_1.14.1           
[28] pkgconfig_2.0.1               XML_3.98-1.9                  biomaRt_2.28.0               
[31] fda_2.4.4                     genefilter_1.54.2             zlibbioc_1.18.0              
[34] xtable_1.8-2                  scales_0.4.1                  BiocParallel_1.6.6           
[37] htmlTable_1.9                 tibble_1.3.3                  annotate_1.50.1              
[40] nnet_7.3-12                   lazyeval_0.2.0                mime_0.5                     
[43] survival_2.41-3               magrittr_1.5                  memoise_1.1.0                
[46] GGally_1.3.1                  foreign_0.8-69                graph_1.50.0                 
[49] tools_3.3.1                   data.table_1.10.4             stringr_1.2.0                
[52] munsell_0.4.3                 locfit_1.5-9.1                cluster_2.0.6                
[55] ensembldb_1.4.7               Biostrings_2.40.2             rlang_0.1.1                  
[58] grid_3.3.1                    RCurl_1.95-4.8                dichromat_2.0-0              
[61] VariantAnnotation_1.18.7      htmlwidgets_0.8               labeling_0.3                 
[64] bitops_1.0-6                  base64enc_0.1-3               gtable_0.2.0                 
[67] DBI_0.7                       reshape_0.8.6                 R6_2.2.2                     
[70] reshape2_1.4.2                GenomicAlignments_1.8.4       gridExtra_2.2.1              
[73] knitr_1.16                    rtracklayer_1.32.2            bit_1.1-12                   
[76] Hmisc_4.0-3                   stringi_1.1.5                 Rcpp_0.12.11                 
[79] geneplotter_1.50.0            rpart_4.1-11                  acepack_1.4.1

Hi Rustavo,

right now I cannot tell what the problem is and from which function it is caused. Could you please run traceback() to track this down.

Best regards,
Felix
 

Rustavo

please first update your R, and use biocLite to install all needed packages. Just to avoid that you're suffering from version mismatches between your installed packages, or that your particular problem has already been fixed.

Wolfgang