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
