roadmap error: Cannot detect format (no extension found in file name)

[bschilder]

Reprex

Code

topSNPs <- echodata::topSNPs_Nalls2019
  fullSS_path <- echodata::example_fullSS(dataset = "Nalls2019")

  res <- echolocatoR::finemap_locus(
    fullSS_path = fullSS_path,
    topSNPs = topSNPs,
    # results_dir = "/Desktop/res",
    locus = "BST1",
    dataset_name = "Nalls2019",
    fullSS_genome_build = "hg19",
    zoom = c("1x","4x"),
    bp_distance = 25000,
    n_causal = 5,
    force_new_finemap = TRUE,
    plot_types = c("simple","fancy","LD"),
    roadmap = TRUE,
    roadmap_query = "E053",
    # nott_epigenome = TRUE,
    # nott_show_placseq = TRUE,
    munged = TRUE)

Console output

 ROADMAP:: 1 annotation(s) identified that match: E053
Querying subset from Roadmap API: E053 - 1/1
Constructing GRanges query using min/max ranges across one or more chromosomes.
+ as_blocks=TRUE: Will query a single range per chromosome that covers all regions requested (plus anything in between).
Downloading Roadmap Chromatin Marks: E053
Preexisting file detected. Set force_overwrite=TRUE to override this.
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'con' in selecting a method for function 'import': Cannot detect format (no extension found in file name)

Session info

``` R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] echolocatoR_2.0.1 snpStats_1.46.0 Matrix_1.4-1 survival_3.4-0

loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 rtracklayer_1.57.0 GGally_2.1.2
[4] R.methodsS3_1.8.2 ragg_1.2.2 tidyr_1.2.0
[7] echoLD_0.99.6 ggplot2_3.3.6 bit64_4.0.5
[10] knitr_1.40 irlba_2.3.5 DelayedArray_0.22.0
[13] R.utils_2.12.0 data.table_1.14.2 rpart_4.1.16
[16] KEGGREST_1.36.3 RCurl_1.98-1.8 AnnotationFilter_1.20.0
[19] generics_0.1.3 BiocGenerics_0.42.0 GenomicFeatures_1.48.3
[22] RSQLite_2.2.16 proxy_0.4-27 bit_4.0.4
[25] tzdb_0.3.0 xml2_1.3.3 SummarizedExperiment_1.26.1
[28] assertthat_0.2.1 viridis_0.6.2 gargle_1.2.0
[31] xfun_0.32 hms_1.1.2 evaluate_0.16
[34] fansi_1.0.3 restfulr_0.0.15 progress_1.2.2
[37] dbplyr_2.2.1 readxl_1.4.1 Rgraphviz_2.40.0
[40] igraph_1.3.4 DBI_1.1.3 htmlwidgets_1.5.4
[43] reshape_0.8.9 downloadR_0.99.4 stats4_4.2.1
[46] purrr_0.3.4 ellipsis_0.3.2 dplyr_1.0.9
[49] backports_1.4.1 biomaRt_2.52.0 deldir_1.0-6
[52] MatrixGenerics_1.8.1 MungeSumstats_1.5.9 vctrs_0.4.1
[55] Biobase_2.56.0 ensembldb_2.20.2 cachem_1.0.6
[58] BSgenome_1.64.0 checkmate_2.1.0 GenomicAlignments_1.32.1
[61] prettyunits_1.1.1 cluster_2.1.4 ape_5.6-2
[64] dir.expiry_1.4.0 lazyeval_0.2.2 crayon_1.5.1
[67] basilisk.utils_1.8.0 crul_1.2.0 labeling_0.4.2
[70] pkgconfig_2.0.3 GenomeInfoDb_1.32.3 nlme_3.1-159
[73] pkgload_1.3.0 ProtGenerics_1.28.0 XGR_1.1.8
[76] nnet_7.3-17 pals_1.7 rlang_1.0.4
[79] lifecycle_1.0.1 filelock_1.0.2 httpcode_0.3.0
[82] BiocFileCache_2.4.0 echotabix_0.99.7 dichromat_2.0-0.1
[85] cellranger_1.1.0 coloc_5.1.0.1 matrixStats_0.62.0
[88] graph_1.74.0 osfr_0.2.8 boot_1.3-28
[91] base64enc_0.1-3 png_0.1-7 viridisLite_0.4.1
[94] rjson_0.2.21 rootSolve_1.8.2.3 bitops_1.0-7
[97] R.oo_1.25.0 ggnetwork_0.5.10 Biostrings_2.64.1
[100] blob_1.2.3 mixsqp_0.3-43 stringr_1.4.1
[103] echoplot_0.99.4 dnet_1.1.7 readr_2.1.2
[106] jpeg_0.1-9 S4Vectors_0.34.0 echodata_0.99.12
[109] scales_1.2.1 memoise_2.0.1 magrittr_2.0.3
[112] plyr_1.8.7 hexbin_1.28.2 zlibbioc_1.42.0
[115] compiler_4.2.1 echoconda_0.99.7 BiocIO_1.6.0
[118] RColorBrewer_1.1-3 EnsDb.Hsapiens.v75_2.99.0 Rsamtools_2.12.0
[121] cli_3.3.0 XVector_0.36.0 echoannot_0.99.7
[124] patchwork_1.1.2 htmlTable_2.4.1 Formula_1.2-4
[127] MASS_7.3-58.1 tidyselect_1.1.2 stringi_1.7.8
[130] textshaping_0.3.6 yaml_2.3.5 supraHex_1.34.0
[133] latticeExtra_0.6-30 ggrepel_0.9.1 grid_4.2.1
[136] VariantAnnotation_1.42.1 tools_4.2.1 lmom_2.9
[139] parallel_4.2.1 rstudioapi_0.14 foreign_0.8-82
[142] piggyback_0.1.4 gridExtra_2.3 gld_2.6.5
[145] farver_2.1.1 RcppZiggurat_0.1.6 digest_0.6.29
[148] BiocManager_1.30.18 Rcpp_1.0.9 GenomicRanges_1.48.0
[151] OrganismDbi_1.38.1 httr_1.4.4 AnnotationDbi_1.58.0
[154] RCircos_1.2.2 ggbio_1.44.1 biovizBase_1.44.0
[157] colorspace_2.0-3 brio_1.1.3 XML_3.99-0.10
[160] fs_1.5.2 reticulate_1.25 IRanges_2.30.1
[163] splines_4.2.1 RBGL_1.72.0 expm_0.999-6
[166] seqminer_8.4 echofinemap_0.99.3 basilisk_1.8.1
[169] Exact_3.1 mapproj_1.2.8 systemfonts_1.0.4
[172] jsonlite_1.8.0 Rfast_2.0.6 testthat_3.1.4
[175] susieR_0.12.19 R6_2.5.1 Hmisc_4.7-1
[178] pillar_1.8.1 htmltools_0.5.3 glue_1.6.2
[181] fastmap_1.1.0 DT_0.24 BiocParallel_1.30.3
[184] class_7.3-20 codetools_0.2-18 maps_3.4.0
[187] mvtnorm_1.1-3 utf8_1.2.2 lattice_0.20-45
[190] tibble_3.1.8 curl_4.3.2 DescTools_0.99.45
[193] zip_2.2.0 openxlsx_4.2.5 interp_1.1-3
[196] rmarkdown_2.16 googleAuthR_2.0.0 munsell_0.5.0
[199] e1071_1.7-11 GenomeInfoDbData_1.2.8 reshape2_1.4.4
[202] gtable_0.3.0

</details>

[bschilder]

This is due to a bug in rtracklayer. I've reached out to the maintainers to try and get it fixed but no response so far:
lawremi/rtracklayer#76

Given this, some options are:

1. Download the entire bed.gz file every time a query is made (highly inefficient but should work)
2. Find an alternative distribution of Roadmap annotations (eg. AnnotationHub) and rewrite echoannot functions accordingly.

[bschilder]

Just implemented workaround 1 (plus some custom bed import scripts that avoid issues with any NAs in the bed file), that doesn't use rtracklayer.