Dear all,
I am trying to use Gviz to plot the H3K27Ac mark as retrieved from the UCSC Genome Browser. So I based my code off the Gviz tutorial for DataTrack-like tracks:
gcContent <- UcscTrack(genome = "mm9",
chromosome = "chrX",
track = "Conservation",
table = "phyloP30wayPlacental",
from = from,
to = to,
trackType = "DataTrack",
start = "start",
end = "end",
data = "score",
type = "mountain",
window = -1,
windowSize = 1500,
fill.histogram = "darkblue",
name = "Conservation")
This works fine. However, when I try my own data, I get the following error:
#Error in DataTrack(chromosome = "chr22", genome = "hg19", name = "H3K27Ac", : # Columns indices for the data section are only allowed when 'range' is of class 'GRanges'
chr <- "chr22"
genome_version <- "hg19"
start <- 50528213
end <- 50528312
h3k27actrack <- UcscTrack(genome = genome_version,
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")
I suspect it has to do with the way the data is saved on the UCSC servers. If I look at the UCSC Table Browser for my specific region of interest (track: "Layered H3K27Ac", table: "wgEncodeBroadHistoneGm12878H3k27acStdSig"), I get the following table:
track type=wiggle_0 name="H1-hESC" description="H3K27Ac Mark (Often Found Near Regulatory Elements) on H1-hESC Cells from ENCODE"
#bedGraph section chr12:9198625-9231075
chr12 9217500 9217525 34.04
chr12 9217525 9217550 33.48
chr12 9217550 9217575 34.36
chr12 9217575 9217600 32.32
chr12 9217600 9217625 29.84
chr12 9217625 9217650 26.28
chr12 9217650 9217675 20.64
This table looks like some sort of BED format table but unfortunately does not have any column names. I believe therefore that
start = "start", end = "end", data = "score",
will not be able to find anything. Is there a way to force UcscTrack to read the "start" as the column 2, "end" as column 3 and "data" as column 4?
sessionInfo() # R version 3.2.3 (2015-12-10) # Platform: x86_64-pc-linux-gnu (64-bit) # Running under: Ubuntu 15.04 # # locale: # [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=nl_NL.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=nl_NL.UTF-8 # [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=nl_NL.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C # [11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C # # attached base packages: # [1] grid stats4 parallel stats graphics grDevices utils datasets methods base # # other attached packages: # [1] Gviz_1.14.0 BiocInstaller_1.20.1 derfinder_1.5.19 GenomicRanges_1.22.3 GenomeInfoDb_1.6.1 IRanges_2.4.6 S4Vectors_0.8.6 # [8] ggbio_1.18.1 ggplot2_2.0.0 BiocGenerics_0.16.1 devtools_1.9.1 # # loaded via a namespace (and not attached): # [1] Biobase_2.30.0 httr_1.0.0 splines_3.2.3 foreach_1.4.3 GenomicFiles_1.6.2 # [6] Formula_1.2-1 bumphunter_1.10.0 latticeExtra_0.6-26 doRNG_1.6 RBGL_1.46.0 # [11] BSgenome_1.38.0 Rsamtools_1.22.0 RSQLite_1.0.0 lattice_0.20-33 biovizBase_1.18.0 # [16] digest_0.6.8 RColorBrewer_1.1-2 XVector_0.10.0 qvalue_2.2.0 colorspace_1.2-6 # [21] Matrix_1.2-3 plyr_1.8.3 OrganismDbi_1.12.1 XML_3.98-1.3 biomaRt_2.26.1 # [26] zlibbioc_1.16.0 xtable_1.8-0 scales_0.3.0 BiocParallel_1.4.3 pkgmaker_0.22 # [31] SummarizedExperiment_1.0.2 GenomicFeatures_1.22.7 nnet_7.3-11 survival_2.38-3 magrittr_1.5 # [36] memoise_0.2.1 GGally_1.0.0 foreign_0.8-66 graph_1.48.0 tools_3.2.3 # [41] registry_0.3 matrixStats_0.50.1 stringr_1.0.0 locfit_1.5-9.1 munsell_0.4.2 # [46] cluster_2.0.3 rngtools_1.2.4 AnnotationDbi_1.32.3 lambda.r_1.1.7 Biostrings_2.38.3 # [51] futile.logger_1.4.1 RCurl_1.95-4.7 dichromat_2.0-0 iterators_1.0.8 VariantAnnotation_1.16.4 # [56] bitops_1.0-6 derfinderHelper_1.4.1 gtable_0.1.2 codetools_0.2-14 DBI_0.3.1 # [61] reshape_0.8.5 curl_0.9.4 reshape2_1.4.1 R6_2.1.1 GenomicAlignments_1.6.3 # [66] gridExtra_2.0.0 knitr_1.11 rtracklayer_1.30.1 Hmisc_3.17-1 futile.options_1.0.0 # [71] stringi_1.0-1 Rcpp_0.12.2 rpart_4.1-10 acepack_1.3-3.3
