Hello! I am currently trying to use one of the built-in reference genomes, mm10, in the GenomicDistributionsData package to make different plots from the GenomicDistributions package for my own analysis. From testing out the example here (https://www.bioconductor.org/packages/devel/bioc/vignettes/GenomicDistributions/inst/doc/intro.html#loading-genomic-range-data), everything worked fine if I used the hg19 genome. The problem came when I tried to change the genome to "mm10" like so:
x = calcChromBinsRef(query, "mm10")
# instead of x = calcChromBinsRef(query, "hg19") which works fine and can plot the correct image
From the GenomicDistributionsData Bioconductor documentation and example HTML, I tried running the following lines to see if mm10 was present in the list of genomes/genome parts, but what returned was "character(0) ":
> datasetListIQR = utils::data(package="GenomicDistributionsData")
> datasetList = datasetListIQR$results[,"Item"]
> datasetList
character(0)
Then I just did things one by one and got the return that there were "no data sets found" when I ran the first line:
utils::data(package="GenomicDistributionsData")
no data sets found
I'm not sure if I'm doing something incorrect or if the mm10 genome isn't loaded yet in the GenomicDistributionsPackage?
Any help is appreciated!!
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] ExperimentHub_2.0.0 AnnotationHub_3.0.2 BiocFileCache_2.0.0
[4] dbplyr_2.2.0 GenomicDistributionsData_1.0.0 ggplot2_3.3.6
[7] biomaRt_2.48.3 dplyr_1.0.9 GenomicDistributions_1.0.0
[10] GenomicRanges_1.44.0 GenomeInfoDb_1.28.4 IRanges_2.26.0
[13] S4Vectors_0.30.2 BiocGenerics_0.38.0
loaded via a namespace (and not attached):
[1] ProtGenerics_1.24.0 bitops_1.0-7 matrixStats_0.62.0
[4] bit64_4.0.5 filelock_1.0.2 progress_1.2.2
[7] httr_1.4.3 tools_4.1.0 utf8_1.2.2
[10] R6_2.5.1 lazyeval_0.2.2 DBI_1.1.3
[13] colorspace_2.0-3 withr_2.5.0 tidyselect_1.1.2
[16] prettyunits_1.1.1 bit_4.0.4 curl_4.3.2
[19] compiler_4.1.0 cli_3.3.0 Biobase_2.52.0
[22] xml2_1.3.3 DelayedArray_0.18.0 rtracklayer_1.52.1
[25] labeling_0.4.2 scales_1.2.0 rappdirs_0.3.3
[28] stringr_1.4.0 digest_0.6.29 Rsamtools_2.8.0
[31] rmarkdown_2.14 XVector_0.32.0 pkgconfig_2.0.3
[34] htmltools_0.5.2 MatrixGenerics_1.4.3 ensembldb_2.16.4
[37] BSgenome_1.60.0 fastmap_1.1.0 rlang_1.0.2
[40] rstudioapi_0.13 RSQLite_2.2.14 shiny_1.7.1
[43] BiocIO_1.2.0 farver_2.1.0 generics_0.1.2
[46] BiocParallel_1.26.2 RCurl_1.98-1.7 magrittr_2.0.3
[49] GenomeInfoDbData_1.2.6 Matrix_1.4-1 Rcpp_1.0.8.3
[52] munsell_0.5.0 fansi_1.0.3 lifecycle_1.0.1
[55] stringi_1.7.6 yaml_2.3.5 SummarizedExperiment_1.22.0
[58] zlibbioc_1.38.0 plyr_1.8.7 grid_4.1.0
[61] blob_1.2.3 promises_1.2.0.1 crayon_1.5.1
[64] lattice_0.20-45 Biostrings_2.60.2 GenomicFeatures_1.44.2
[67] hms_1.1.1 KEGGREST_1.32.0 knitr_1.39
[70] pillar_1.7.0 rjson_0.2.21 reshape2_1.4.4
[73] BiocVersion_3.13.1 XML_3.99-0.10 glue_1.6.2
[76] evaluate_0.15 data.table_1.14.2 BiocManager_1.30.18
[79] httpuv_1.6.5 vctrs_0.4.1 png_0.1-7
[82] gtable_0.3.0 purrr_0.3.4 assertthat_0.2.1
[85] cachem_1.0.6 xfun_0.31 mime_0.12
[88] xtable_1.8-6 AnnotationFilter_1.16.0 restfulr_0.0.15
[91] later_1.3.0 tibble_3.1.7 GenomicAlignments_1.28.0
[94] AnnotationDbi_1.54.1 memoise_2.0.1 interactiveDisplayBase_1.30.0
[97] ellipsis_0.3.2
You need to give more information about what happened when you ran
calcChromBinsRef
rather than what you did to try to diagnose (for example, there are no datasets in theGenomicDistributionData
package - it just helps find data on theExperimentHub
). Anyway,calcChromBinsRef
will callgetChromSizes
, which needs aBSGenome
package for mm10 to work. R probably told you something after you tried to runcalcChromBinsRef
but you don't say what that was. Without that information we can only guess. You want to provide enough information so we don't have to do that.Thank you. Apologies for not providing more information; I'm pretty new at this! Below is what happens when I run
calcChromBinsRef
.session info:
Weird. It looks like the maintainer has been changing from providing the data as part of the package (which is a bad idea) to hosting the data on the ExperimentHub (good idea!). But the code hasn't been updated to actually use the ExperimentHub. As you are apparently aware, the code currently looks for data in the
GenomicDistributions
package, and if not there, it looks inGenomicDistributionsData
. But what is inGenomicDistributionsData
are functions to get the data from the ExperimentHub:This is all helpfully explained in the vignette. But so far as I can tell you can't pass that information in. I would contact the maintainer directly and complain. In the intervening period, here's some hack action.
Oh, also. You need to upgrade to the current version of R/Bioconductor. You are two releases behind, and technically we don't support old versions.
Thank you so much!! Using the debugging approach is working great for me in the meantime while I wait on the author's response to upload the mm10 genome into ExperimentHub.
Also, thank you for letting me know to update R/BioConductor. Did that before trying all of this.