Question: Error GC content and conservation visualization with Gviz
0
gravatar for h
17 months ago by
h0
h0 wrote:

Hi,

I recently discovered the Gviz package, which I find extremely flexible and easy to use! 
I was wondering if somebody could help with two errors which I don't understand. They concern the following bit of code: 

chr <- 3
from <- 48938762 
to <- 49886319

gcContent <- UcscTrack(genome = "hg19", chromosome = paste0("chr", chr),
                       track = "GC Percent", table = "gc5Base", from = from,
                       to = to, trackType = "DataTrack", start = "start",
                       end = "end", data = "score", type = "hist", window = -1,
                       windowSize = 1500, fill.histogram = "black",
                       col.histogram = "black", ylim = c(30, 70), name = "GC Percent")

Error in UcscTrack(genome = "hg19", chromosome = paste0("chr", chr), track = "GC Percent",  : 
  Error fetching data from UCSC
In addition: Warning messages:
1: In matrix(as.numeric(unlist(split_lines)), nrow = 2) :
  NAs introduced by coercion
2: In matrix(as.numeric(unlist(split_lines)), nrow = 2) :
  data length [200005] is not a sub-multiple or multiple of the number of rows [2]
3: In UcscTrack(genome = "hg19", chromosome = paste0("chr", chr), track = "GC Percent",  :
  Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 100001: range cannot be determined from the supplied arguments (too many NAs)

conservation <- UcscTrack(genome = "hg19", chromosome = paste0("chr", chr),
                          track = "Conservation", table = "multiz100way",
                          from = from, to = to, trackType = "DataTrack",
                          start = "start", end = "end", # data = "score",
                          type = "hist", window = "auto", col.histogram = "darkblue",
                          fill.histogram = "darkblue", ylim = c(-3.7, 4),
                          name = "Conservation")
Error in UcscTrack(genome = "hg19", chromosome = paste0("chr", chr), track = "Conservation",  : 
  Error fetching data from UCSC
In addition: Warning message:
In UcscTrack(genome = "hg19", chromosome = paste0("chr", chr), track = "Conservation",  :
  Error in .local(object, ...) : No supported output types

For the GC content, I got no error when I used a smaller chunk, i.e., replacing in the above:

to <- 49100000

The "conservation" part produces an error anyway..

Any idea on why this happens and on how I could solve this?

Thanks!

 

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.3 (Maipo)

Matrix products: default
BLAS: /Software/R/R-3.4.3-gcc/lib64/R/lib/libRblas.so
LAPACK: /Software/R/R-3.4.3-gcc/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] Homo.sapiens_1.3.1                      org.Hs.eg.db_3.5.0                     
 [3] GO.db_3.5.0                             OrganismDbi_1.20.0                     
 [5] BiocInstaller_1.28.0                    TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [7] GenomicFeatures_1.30.3                  AnnotationDbi_1.40.0                   
 [9] Biobase_2.38.0                          Gviz_1.22.3                            
[11] GenomicRanges_1.30.3                    GenomeInfoDb_1.14.0                    
[13] IRanges_2.12.0                          S4Vectors_0.16.0                       
[15] BiocGenerics_0.24.0                    

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.10.0           bitops_1.0-6                  matrixStats_0.53.1           
 [4] bit64_0.9-7                   RColorBrewer_1.1-2            progress_1.1.2               
 [7] httr_1.3.1                    tools_3.4.3                   backports_1.1.2              
[10] R6_2.2.2                      rpart_4.1-11                  Hmisc_4.1-1                  
[13] DBI_0.7                       lazyeval_0.2.1                colorspace_1.3-2             
[16] nnet_7.3-12                   gridExtra_2.3                 prettyunits_1.0.2            
[19] RMySQL_0.10.14                bit_1.1-12                    curl_3.1                     
[22] compiler_3.4.3                graph_1.56.0                  htmlTable_1.11.2             
[25] DelayedArray_0.4.1            rtracklayer_1.38.3            scales_0.5.0                 
[28] checkmate_1.8.5               RBGL_1.54.0                   stringr_1.2.0                
[31] digest_0.6.15                 Rsamtools_1.30.0              foreign_0.8-69               
[34] XVector_0.18.0                base64enc_0.1-3               dichromat_2.0-0              
[37] pkgconfig_2.0.1               htmltools_0.3.6               ensembldb_2.2.2              
[40] BSgenome_1.46.0               htmlwidgets_1.0               rlang_0.1.6                  
[43] rstudioapi_0.7                RSQLite_2.0                   shiny_1.0.5                  
[46] BiocParallel_1.12.0           acepack_1.4.1                 VariantAnnotation_1.24.5     
[49] RCurl_1.95-4.10               magrittr_1.5                  GenomeInfoDbData_1.0.0       
[52] Formula_1.2-2                 Matrix_1.2-12                 Rcpp_0.12.15                 
[55] munsell_0.4.3                 stringi_1.1.6                 yaml_2.1.16                  
[58] SummarizedExperiment_1.8.1    zlibbioc_1.24.0               plyr_1.8.4                   
[61] AnnotationHub_2.10.1          blob_1.1.0                    lattice_0.20-35              
[64] Biostrings_2.46.0             splines_3.4.3                 knitr_1.20                   
[67] pillar_1.1.0                  reshape2_1.4.3                biomaRt_2.34.2               
[70] XML_3.98-1.10                 biovizBase_1.26.0             latticeExtra_0.6-28          
[73] data.table_1.10.4-3           httpuv_1.3.5                  gtable_0.2.0                 
[76] assertthat_0.2.0              ggplot2_2.2.1                 mime_0.5                     
[79] xtable_1.8-2                  AnnotationFilter_1.2.0        survival_2.41-3              
[82] tibble_1.4.2                  GenomicAlignments_1.14.2      memoise_1.1.0                
[85] cluster_2.0.6                 interactiveDisplayBase_1.16.0
gviz gviz-package • 320 views
ADD COMMENTlink modified 17 months ago by Robert Ivanek640 • written 17 months ago by h0
Answer: Error GC content and conservation visualization with Gviz
0
gravatar for Robert Ivanek
17 months ago by
Robert Ivanek640
Switzerland
Robert Ivanek640 wrote:

Hi,

I believe it is caused by the fact that UCSC does not allow you to fetch large hunks of data (it is also mentioned in the rtracklayer vignette). Either you need to download the files from FTP and read them into Gviz or fetch the data in small chunks and combine afterwards. 

Best, Robert

ADD COMMENTlink written 17 months ago by Robert Ivanek640
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