Question: Gviz - UcscTrack
0
gravatar for cardenasca
2.4 years ago by
cardenasca40
cardenasca40 wrote:

Hello,

I have the following error after trying to load the Layered H3K27Ac track from UCSC genome browser. Any ideas as to why this will occur?

 

Thank you!

> h3k27actrack <- UcscTrack(genome = gen,
+                             chromosome = chr,
+                             track = "Layered H3K27Ac",
+                             table = "wgEncodeBroadHistoneGm12878H3k27acStdSig",
+                             from = start,
+                             to = end,
+                             trackType = "DataTrack",
+                             start = "start",
+                             end = "end",
+                             data = "score",
+                             type = "hist",
+                             window = -1,
+                             windowSize = 1500,
+                             fill.histogram = "black",
+                             name = "H3K27Ac")
Error in UcscTrack(genome = gen, chromosome = chr, track = "Layered H3K27Ac",  : 
  Error fetching data from UCSC
In addition: Warning message:
In UcscTrack(genome = gen, chromosome = chr, track = "Layered H3K27Ac",  :
  Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  scan() expected 'an integer', got 'section'

 

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] colortools_0.1.5                                    rtracklayer_1.34.1                                 
 [3] coMET_1.6.0                                         trackViewer_1.10.2                                 
 [5] ggbio_1.22.3                                        psych_1.6.12                                       
 [7] biomaRt_2.30.0                                      Gviz_1.18.1                                        
 [9] lmtest_0.9-34                                       zoo_1.7-14                                         
[11] sandwich_2.3-4                                      MASS_7.3-45                                        
[13] Hmisc_4.0-2                                         ggplot2_2.2.1                                      
[15] Formula_1.2-1                                       survival_2.40-1                                    
[17] lattice_0.20-34                                     qvalue_2.6.0                                       
[19] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0 minfi_1.20.2                                       
[21] bumphunter_1.14.0                                   locfit_1.5-9.1                                     
[23] iterators_1.0.8                                     foreach_1.4.3                                      
[25] Biostrings_2.42.1                                   XVector_0.14.0                                     
[27] SummarizedExperiment_1.4.0                          GenomicRanges_1.26.2                               
[29] GenomeInfoDb_1.10.2                                 IRanges_2.8.1                                      
[31] S4Vectors_0.12.1                                    Biobase_2.34.0                                     
[33] BiocGenerics_0.20.0                                 qqman_0.1.2                                        
[35] corrplot_0.77                                      

loaded via a namespace (and not attached):
 [1] colorspace_1.3-2              siggenes_1.48.0               mclust_5.2.1                  biovizBase_1.22.0            
 [5] htmlTable_1.8                 base64enc_0.1-3               dichromat_2.0-0               base64_2.0                   
 [9] hash_2.2.6                    interactiveDisplayBase_1.12.0 AnnotationDbi_1.36.1          codetools_0.2-15             
[13] splines_3.3.2                 mnormt_1.5-5                  knitr_1.15.1                  Rsamtools_1.26.1             
[17] annotate_1.52.1               cluster_2.0.5                 grImport_0.9-0                graph_1.52.0                 
[21] shiny_1.0.0                   httr_1.2.1                    backports_1.0.5               assertthat_0.1               
[25] Matrix_1.2-8                  lazyeval_0.2.0                limma_3.30.8                  acepack_1.4.1                
[29] htmltools_0.3.5               tools_3.3.2                   gtable_0.2.0                  reshape2_1.4.2               
[33] doRNG_1.6                     Rcpp_0.12.9                   multtest_2.30.0               preprocessCore_1.36.0        
[37] nlme_3.1-128                  stringr_1.1.0                 mime_0.5                      ensembldb_1.6.2              
[41] rngtools_1.2.4                XML_3.98-1.5                  beanplot_1.2                  AnnotationHub_2.6.4          
[45] zlibbioc_1.20.0               scales_0.4.1                  BSgenome_1.42.0               VariantAnnotation_1.20.2     
[49] BiocInstaller_1.24.0          RBGL_1.50.0                   GEOquery_2.40.0               RColorBrewer_1.1-2           
[53] yaml_2.1.14                   pbapply_1.3-1                 memoise_1.0.0                 gridExtra_2.2.1              
[57] pkgmaker_0.22                 rpart_4.1-10                  reshape_0.8.6                 latticeExtra_0.6-28          
[61] stringi_1.1.2                 RSQLite_1.1-2                 genefilter_1.56.0             checkmate_1.8.2              
[65] GenomicFeatures_1.26.2        BiocParallel_1.8.1            matrixStats_0.51.0            bitops_1.0-6                 
[69] nor1mix_1.2-2                 GenomicAlignments_1.10.0      GGally_1.3.0                  plyr_1.8.4                   
[73] magrittr_1.5                  R6_2.2.0                      DBI_0.5-1                     foreign_0.8-67               
[77] RCurl_1.95-4.8                nnet_7.3-12                   tibble_1.2                    OrganismDbi_1.16.0           
[81] data.table_1.10.0             digest_0.6.11                 xtable_1.8-2                  httpuv_1.3.3                 
[85] illuminaio_0.16.0             openssl_0.9.6                 munsell_0.4.3                 registry_0.3                 
[89] quadprog_1.5-5   

 

 

 

gviz comet • 701 views
ADD COMMENTlink modified 19 months ago by Tiphaine Martin40 • written 2.4 years ago by cardenasca40
Answer: Gviz - UcscTrack
1
gravatar for Tiphaine Martin
19 months ago by
France
Tiphaine Martin40 wrote:

Hi,

This error and related to the link between Gviz and UCSC

When I apply with this general features (it better that you give us your area that you want to visualize)

gen <- "hg19"
 chr <- "chr2"
 start <- 38290160
end <- 38303219

I have another error message :

Error in UcscTrack(genome = gen, chromosome = chr, track = "Layered H3K27Ac",  : 
  Error fetching data from UCSC
In addition: Warning message:
In UcscTrack(genome = gen, chromosome = chr, track = "Layered H3K27Ac",  :
  Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 261 did not have 4 elements

 

if you request data in UCSC you can see in their table that there is a strange value 

chr2	38297875	38297900	3.12
#bedGraph section chr2:38297900-38333225
chr2	38297900	38297925	3.48
chr2	38297925	38297950	4.48

So need to contact UCSC for this issue !

Regards,

Tiphaine 

ADD COMMENTlink written 19 months ago by Tiphaine Martin40
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