Hi,
I am following the "Example 1: the RepeatMasker Track" given by Michael Lawrence in chapter 5.1 of the documentation for the package 'rtracklayer':
library (rtracklayer)
mySession = browserSession("UCSC")
genome(mySession) <- "hg19"
e2f3.tss.grange <- GRanges("chr6", IRanges(20400587, 20403336))
tbl.rmsk <- getTable(
ucscTableQuery(mySession, track="rmsk",
range=e2f3.tss.grange, table="rmsk"))
Running this code, I get the error message: "error in evaluating the argument 'object' in selecting a method for function 'getTable': error in evaluating the argument 'table' in selecting a method for function '%in%': Unknown track: rmsk"
Listing all available tracks reveals that the name for the track might be: "RepeatMasker".
# List all available tracks in the session
available_tracks <- trackNames(mySession)
print("Available Tracks:")
print(sort(available_tracks))
However, when I replace the track name "rmsk" with "RepeatMasker (see below), I still get an error message:
library (rtracklayer)
mySession = browserSession("UCSC")
genome(mySession) <- "hg19"
e2f3.tss.grange <- GRanges("chr6", IRanges(20400587, 20403336))
tbl.rmsk <- getTable(
ucscTableQuery(mySession, track="RepeatMasker",
range=e2f3.tss.grange, table="rmsk"))
command: tbl.rmsk <- getTable(...) error message: "Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': second argument must be a list"
How can I get the example to work?
Kind regards, Andreas
sessioninfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtracklayer_1.64.0 GenomicRanges_1.56.1 GenomeInfoDb_1.40.1 IRanges_2.38.1 S4Vectors_0.42.1 BiocGenerics_0.50.0
loaded via a namespace (and not attached):
[1] utf8_1.2.4 generics_0.1.3 SparseArray_1.4.8 bitops_1.0-8 lattice_0.22-6 digest_0.6.37 magrittr_2.0.3
[8] grid_4.4.1 evaluate_1.0.0 fastmap_1.2.0 Matrix_1.7-0 jsonlite_1.8.8 restfulr_0.0.15 httr_1.4.7
[15] fansi_1.0.6 UCSC.utils_1.0.0 XML_3.99-0.17 Biostrings_2.72.1 codetools_0.2-20 abind_1.4-8 cli_3.6.3
[22] rlang_1.1.4 crayon_1.5.3 XVector_0.44.0 Biobase_2.64.0 DelayedArray_0.30.1 yaml_2.3.10 S4Arrays_1.4.1
[29] tools_4.4.1 parallel_4.4.1 BiocParallel_1.38.0 dplyr_1.1.4 GenomeInfoDbData_1.2.12 Rsamtools_2.20.0 SummarizedExperiment_1.34.0
[36] curl_5.2.2 vctrs_0.6.5 R6_2.5.1 matrixStats_1.4.1 BiocIO_1.14.0 lifecycle_1.0.4 zlibbioc_1.50.0
[43] pkgconfig_2.0.3 pillar_1.9.0 glue_1.7.0 xfun_0.47 tibble_3.2.1 GenomicAlignments_1.40.0 tidyselect_1.2.1
[50] MatrixGenerics_1.16.0 rstudioapi_0.16.0 knitr_1.48 rjson_0.2.23 htmltools_0.5.8.1 rmarkdown_2.28 compiler_4.4.1
[57] RCurl_1.98-1.16
Dear James,
thank you very much for your response! Your solution is working.
However, it turned out that neither the command 'tbl.rmsk <- getTable(ucscTableQuery(mySession, table = "rmsk", range = e2f3.tss.grange))' nor 'tbl.rmsk <- getTable(ucscTableQuery(mySession, track="RepeatMasker", range=e2f3.tss.grange, table="rmsk"))' were working in the first place due to a problem with the company proxy server.
Kind regards, Andreas