getTable() produces a Bad Request error

[yige-luo]

Hi @lawremi

I'm following a GWA tutorial by Reed et al., 2015 and learning how to make regional association plots for candidates SNPs around CETP gene locus. Query "uc002eki.2" and"uc002ekj.2" can be retrieved directly from UCSC genome browser and seem to be two haplotypes of CETP.

However, I also have problem with getTable() - it returns the same "Bad Request" error when I tried to get some UCSC tables e.g.:

library(rtracklayer) session <- browserSession() genome <- "hg19" chromosome <- "chr16" maxRange <- 57022352L minRange <- 56990716L tbl <- "kgXref" query2 <- ucscTableQuery(session, "knownGene", GRangesForUCSCGenome(genome, chromosome, IRanges::IRanges(minRange, maxRange)), table = tbl, names = c("uc002eki.2", "uc002ekj.2")) t1 <- getTable(query2)

My session info is as follows()

R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

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

other attached packages: [1] Hmisc_4.4-0 Formula_1.2-3 survival_3.1-8 lattice_0.20-38 forcats_0.4.0 stringr_1.4.0
[7] dplyr_0.8.3 purrr_0.3.4 readr_1.3.1 tidyr_1.0.0 tibble_2.1.3 tidyverse_1.2.1 [13] ggplot2_3.2.1

loaded via a namespace (and not attached): [1] Rcpp_1.0.2 lubridate_1.7.4 png_0.1-7 assertthat_0.2.1 digest_0.6.25
[6] R6_2.4.1 cellranger_1.1.0 backports_1.1.4 acepack_1.4.1 httr_1.4.1
[11] pillar_1.4.2 rlang_0.4.6 lazyeval_0.2.2 readxl_1.3.1 data.table_1.12.8
[16] rstudioapi_0.11 rpart_4.1-15 Matrix_1.2-18 checkmate_1.9.4 labeling_0.3
[21] splines_3.6.3 foreign_0.8-75 htmlwidgets_1.5.1 munsell_0.5.0 broom_0.5.3
[26] compiler_3.6.3 modelr_0.1.5 xfun_0.11 pkgconfig_2.0.3 base64enc_0.1-3
[31] htmltools_0.4.0 nnet_7.3-12 tidyselect_0.2.5 gridExtra_2.3 htmlTable_2.0.0
[36] fansi_0.4.0 crayon_1.3.4 withr_2.1.2 grid_3.6.3 nlme_3.1-144
[41] jsonlite_1.6.1 gtable_0.3.0 lifecycle_0.1.0 magrittr_1.5 scales_1.0.0
[46] cli_2.0.2 stringi_1.4.3 latticeExtra_0.6-29 xml2_1.2.2 generics_0.0.2
[51] vctrs_0.3.1 RColorBrewer_1.1-2 tools_3.6.3 glue_1.4.1 hms_0.5.2
[56] jpeg_0.1-8.1 yaml_2.2.0 colorspace_1.4-1 cluster_2.1.0 rvest_0.3.5
[61] knitr_1.26 haven_2.1.1

I'm new to Bioconductor packages and probably not understand the black boxes. Could you help me with this problem?

Sincerely, Yige

[mcneney]

FWIW, I can reproduce the error on my Linux laptop with R 4.0.2:

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 grid stats graphics grDevices utils
[8] datasets methods base

other attached packages: [1] rtracklayer_1.48.0 GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 [4] IRanges_2.22.2 S4Vectors_0.26.1 BiocGenerics_0.34.0 [7] snpStats_1.38.0 Matrix_1.2-18 survival_3.1-12
[10] LDheatmap_0.99-7

loaded via a namespace (and not attached): [1] Rcpp_1.0.4.6 rstudioapi_0.11
[3] XVector_0.28.0 splines_4.0.2
[5] zlibbioc_1.34.0 GenomicAlignments_1.24.0
[7] BiocParallel_1.22.0 lattice_0.20-41
[9] tools_4.0.2 SummarizedExperiment_1.18.1 [11] Biobase_2.48.0 matrixStats_0.56.0
[13] crayon_1.3.4 GenomeInfoDbData_1.2.3
[15] bitops_1.0-6 RCurl_1.98-1.2
[17] DelayedArray_0.14.0 compiler_4.0.2
[19] Biostrings_2.56.0 Rsamtools_2.4.0
[21] XML_3.99-0.3

[yige-luo]

any update on this?

[mcneney]

A user of the LDheatmap package that depends on rtracklayer reports that queries with ucscTableQuery succeed if you omit the names argument.

[lawremi]

Unfortunately, I'm unable to reproduce this. Within the next few months, the entire table browser client will be replaced (internally) by a client to the UCSC REST API, so this bug will soon be obsolete.

[mcneney]

Thanks for the update.