Unable to reproduce the example data eqtl plot

[vivekruhela]

Hi,

I am trying to generate the eqtl plots for the example data. I am following the instructions as mentioned in the README but still not able to reproduce it. The commands and session information of R is shown below:

eQTpLot(GWAS.df = GWAS.df.example, eQTL.df = eQTL.df.example, gene = c("BBS1", "ACTN3"),
gbuild = "hg19", trait = "LDL", tissue = "all", CollapseMethod = "min",
GeneList = T)
[1] "Checking input data..."
[1] "PHE column found in GWAS.df. Analyzing data for phenotype LDL"
[1] "PanTissue eQTL analysis, collapsing by method min will be completed across all tissues in eQTL.df"
[1] "For genes:"
[1] "'BBS1', 'ACTN3'"
[1] "eQTL analysis for gene BBS1: Pearson correlation: 0.823, p-value: 1.62e-127"
[2] "eQTL analysis for gene ACTN3: Pearson correlation: 0.245, p-value: 1.52e-07"
[1] "Complete"

eQTpLot(GWAS.df = GWAS.df.example, eQTL.df = eQTL.df.example, gene = "BBS1",
gbuild = "hg19", trait = "LDL", tissue = "all", CollapseMethod = "min")
[1] "Checking input data..."
[1] "PHE column found in GWAS.df. Analyzing data for phenotype LDL"
[1] "Compiling GWAS and eQTL data..."
[1] "eQTL analysis will be completed for tissues 'all' and for gene BBS1"
[1] "Generating main plot..."
[1] "Generating gene tracks..."
Error in collect():
! Failed to collect lazy table.
Caused by error in db_collect():
! Arguments in ... must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
Run rlang::last_trace() to see where the error occurred.

sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS: /mnt/vast/hpc/mgmt/apps/R-4.2.2.10/lib/libRblas.so
LAPACK: /mnt/vast/hpc/mgmt/apps/R-4.2.2.10/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] splines stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] aGE_0.0.0.9000 eQTpLot_0.0.0.9000 ggplot2_3.5.1 devtools_2.4.5
[5] usethis_2.2.3 snpStats_1.48.0 Matrix_1.6-5 survival_3.5-8
[9] haplo.stats_1.9.7 arsenal_3.6.3 MASS_7.3-60.0.1 readxl_1.4.3
[13] Haplin_7.3.2 VGAM_1.1-12 PResiduals_1.0-1 org.Hs.eg.db_3.16.0
[17] AnnotationDbi_1.60.2 IRanges_2.32.0 S4Vectors_0.36.2 Biobase_2.58.0
[21] BiocGenerics_0.44.0 genio_1.1.2 tidyr_1.3.1 dplyr_1.1.4

loaded via a namespace (and not attached):
[1] backports_1.5.0 Hmisc_5.2-0 BiocFileCache_2.6.1
[4] lazyeval_0.2.2 BiocParallel_1.32.6 GenomeInfoDb_1.34.9
[7] TH.data_1.1-2 digest_0.6.37 ensembldb_2.22.0
[10] htmltools_0.5.8.1 fansi_1.0.6 magrittr_2.0.3
[13] checkmate_2.3.2 memoise_2.0.1 BSgenome_1.66.3
[16] cluster_2.1.6 remotes_2.5.0 Biostrings_2.66.0
[19] matrixStats_1.2.0 sandwich_3.1-1 prettyunits_1.2.0
[22] jpeg_0.1-10 colorspace_2.1-1 blob_1.2.4
[25] rappdirs_0.3.3 xfun_0.47 crayon_1.5.2
[28] RCurl_1.98-1.14 VariantAnnotation_1.44.1 zoo_1.8-12
[31] glue_1.7.0 gtable_0.3.6 zlibbioc_1.44.0
[34] XVector_0.38.0 MatrixModels_0.5-3 DelayedArray_0.24.0
[37] pkgbuild_1.4.4 rms_6.8-0 SparseM_1.84-2
[40] scales_1.3.0 mvtnorm_1.3-2 DBI_1.2.2
[43] miniUI_0.1.1.1 Rcpp_1.0.13-1 viridisLite_0.4.2
[46] xtable_1.8-4 progress_1.2.3 htmlTable_2.4.3
[49] foreign_0.8-86 bit_4.0.5 Formula_1.2-5
[52] profvis_0.3.8 htmlwidgets_1.6.4 httr_1.4.7
[55] RColorBrewer_1.1-3 ellipsis_0.3.2 ff_4.5.0
[58] farver_2.1.2 urlchecker_1.0.1 pkgconfig_2.0.3
[61] XML_3.99-0.16.1 deldir_2.0-4 Gviz_1.42.1
[64] nnet_7.3-19 dbplyr_2.5.0 utf8_1.2.4
[67] tidyselect_1.2.1 rlang_1.1.4 later_1.3.2
[70] munsell_0.5.1 cellranger_1.1.0 tools_4.2.2
[73] cachem_1.0.8 cli_3.6.3 generics_0.1.3
[76] RSQLite_2.3.5 evaluate_1.0.1 stringr_1.5.1
[79] fastmap_1.1.1 yaml_2.3.10 knitr_1.48
[82] bit64_4.0.5 fs_1.6.3 purrr_1.0.2
[85] AnnotationFilter_1.22.0 KEGGREST_1.38.0 nlme_3.1-164
[88] mime_0.12 quantreg_5.99.1 xml2_1.3.6
[91] biomaRt_2.54.1 compiler_4.2.2 rstudioapi_0.17.1
[94] filelock_1.0.3 curl_5.2.1 png_0.1-8
[97] tibble_3.2.1 stringi_1.8.4 GenomicFeatures_1.50.4
[100] lattice_0.22-6 ProtGenerics_1.30.0 vctrs_0.6.5
[103] pillar_1.9.0 lifecycle_1.0.4 data.table_1.16.2
[106] bitops_1.0-7 rtracklayer_1.58.0 httpuv_1.6.15
[109] GenomicRanges_1.50.2 latticeExtra_0.6-30 BiocIO_1.8.0
[112] R6_2.5.1 promises_1.3.0 gridExtra_2.3
[115] sessioninfo_1.2.2 codetools_0.2-19 dichromat_2.0-0.1
[118] polspline_1.1.25 pkgload_1.3.4 SummarizedExperiment_1.28.0
[121] rjson_0.2.21 withr_3.0.2 GenomicAlignments_1.34.1
[124] Rsamtools_2.14.0 multcomp_1.4-26 GenomeInfoDbData_1.2.9
[127] mgcv_1.9-1 parallel_4.2.2 hms_1.1.3
[130] grid_4.2.2 rpart_4.1.23 rmarkdown_2.29
[133] MatrixGenerics_1.10.0 biovizBase_1.46.0 shiny_1.9.1
[136] base64enc_0.1-3 interp_1.1-6 restfulr_0.0.15

Could you please suggest what is the possible issue. Thanks

[TGDrivas]

Hello,

I just did a fresh install of eQTpLot and all its dependencies and was unable to reproduce the error; it ran as expected. I would imagine the issue has to do with versions and compatibilities of the different R packages required, and would recommend updating these if possible, and considering updating R as well.

[vivekruhela]

Hi, I am using the updated R Studio with R version 4.4.2 but still not able to reproduce the example data eqtl plot. Here is the code:

`> library(eQTpLot)

data(GWAS.df.example)
head(GWAS.df.example)
CHR BP SNP P BETA PHE
1 11 66078129 rs1625595 0.06646 -7.925e-05 Creatinine
2 11 66078252 rs565374903 0.17350 -1.915e-02 Creatinine
3 11 66078296 rs750544051 0.03073 -4.299e-02 Creatinine
4 11 66078347 11:66078347_C_G 0.64030 -9.298e-03 Creatinine
5 11 66078368 rs541384459 0.93890 5.763e-04 Creatinine
6 11 66078385 rs138591375 0.34690 1.647e-03 Creatinine
data(eQTL.df.example)
data(Genes.df.example)
eQTpLot(GWAS.df = GWAS.df.example, eQTL.df = eQTL.df.example, gene = c("BBS1", "ACTN3"),
gbuild = "hg19", trait = "LDL", tissue = "all", CollapseMethod = "min",
GeneList = T)
[1] "Checking input data..."
[1] "PHE column found in GWAS.df. Analyzing data for phenotype LDL"
[1] "PanTissue eQTL analysis, collapsing by method min will be completed across all tissues in eQTL.df"
[1] "For genes:"
[1] "'BBS1', 'ACTN3'"
[1] "eQTL analysis for gene BBS1: Pearson correlation: 0.823, p-value: 1.62e-127"
[2] "eQTL analysis for gene ACTN3: Pearson correlation: 0.245, p-value: 1.52e-07"
[1] "Complete"
eQTpLot(GWAS.df = GWAS.df.example, eQTL.df = eQTL.df.example, gene = "BBS1",
gbuild = "hg19", trait = "LDL", tissue = "all", CollapseMethod = "min")
[1] "Checking input data..."
[1] "PHE column found in GWAS.df. Analyzing data for phenotype LDL"
[1] "Compiling GWAS and eQTL data..."
[1] "eQTL analysis will be completed for tissues 'all' and for gene BBS1"
[1] "Generating main plot..."
Warning: The <scale> argument of guides() cannot be FALSE. Use "none" instead as of
ggplot2 3.3.4.
ℹ The deprecated feature was likely used in the eQTpLot package.
Please report the issue to the authors.
This warning is displayed once every 8 hours.
Call lifecycle::last_lifecycle_warnings() to see where this warning was
generated.
[1] "Generating gene tracks..."
Error in req_perform():
! Failed to perform HTTP request.
Caused by error in curl::curl_fetch_memory():
! Timeout was reached [grch37.ensembl.org]: Connection timed out after 60000 milliseconds
Run rlang::last_trace() to see where the error occurred.

sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS: /mnt/vast/hpc/mgmt/apps/DEBIAN12/R-4.4.2/lib/R/lib/libRblas.so
LAPACK: /mnt/vast/hpc/mgmt/apps/DEBIAN12/R-4.4.2/lib/R/lib/libRlapack.so; LAPACK version 3.12.0

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

time zone: America/New_York
tzcode source: system (glibc)

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

other attached packages:
[1] eQTpLot_0.0.0.9000 writexl_1.5.1
[3] pbapply_1.7-2 pheatmap_1.0.12
[5] circlize_0.4.16 DESeq2_1.46.0
[7] SummarizedExperiment_1.36.0 Biobase_2.66.0
[9] MatrixGenerics_1.18.0 matrixStats_1.4.1
[11] GenomicRanges_1.58.0 GenomeInfoDb_1.42.1
[13] IRanges_2.40.1 S4Vectors_0.44.0
[15] BiocGenerics_0.52.0 DT_0.33
[17] ComplexHeatmap_2.22.0 shiny_1.10.0
[19] genio_1.1.2 ggrepel_0.9.6
[21] ggsci_3.2.0 scales_1.3.0
[23] hrbrthemes_0.8.7 cowplot_1.1.3
[25] lubridate_1.9.4 forcats_1.0.0
[27] stringr_1.5.1 purrr_1.0.2
[29] readr_2.1.5 tidyr_1.3.1
[31] tibble_3.2.1 tidyverse_2.0.0
[33] Cairo_1.6-2 CMplot_4.5.1
[35] qqman_0.1.9 readxl_1.4.3
[37] ggplot2_3.5.1 dplyr_1.1.4

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_1.8.9
[4] shape_1.4.6.1 magrittr_2.0.3 farver_2.1.2
[7] rmarkdown_2.29 GlobalOptions_0.1.2 zlibbioc_1.52.0
[10] ragg_1.3.3 vctrs_0.6.5 memoise_2.0.1
[13] progress_1.2.3 htmltools_0.5.8.1 S4Arrays_1.6.0
[16] curl_6.0.1 cellranger_1.1.0 SparseArray_1.6.0
[19] sass_0.4.9 bslib_0.8.0 htmlwidgets_1.6.4
[22] httr2_1.0.7 cachem_1.1.0 mime_0.12
[25] lifecycle_1.0.4 iterators_1.0.14 pkgconfig_2.0.3
[28] Matrix_1.7-1 R6_2.5.1 fastmap_1.2.0
[31] GenomeInfoDbData_1.2.13 clue_0.3-66 digest_0.6.37
[34] colorspace_2.1-1 AnnotationDbi_1.68.0 pkgload_1.4.0
[37] textshaping_0.4.1 RSQLite_2.3.9 filelock_1.0.3
[40] labeling_0.4.3 timechange_0.3.0 httr_1.4.7
[43] abind_1.4-8 compiler_4.4.2 bit64_4.5.2
[46] fontquiver_0.2.1 withr_3.0.2 doParallel_1.0.17
[49] BiocParallel_1.40.0 DBI_1.2.3 Rttf2pt1_1.3.12
[52] biomaRt_2.62.0 MASS_7.3-61 rappdirs_0.3.3
[55] DelayedArray_0.32.0 rjson_0.2.23 tools_4.4.2
[58] httpuv_1.6.15 extrafontdb_1.0 glue_1.8.0
[61] promises_1.3.2 cluster_2.1.6 generics_0.1.3
[64] gtable_0.3.6 tzdb_0.4.0 hms_1.1.3
[67] xml2_1.3.6 XVector_0.46.0 foreach_1.5.2
[70] pillar_1.10.0 later_1.4.1 BiocFileCache_2.14.0
[73] lattice_0.22-6 bit_4.5.0.1 tidyselect_1.2.1
[76] fontLiberation_0.1.0 locfit_1.5-9.10 Biostrings_2.74.1
[79] knitr_1.49 fontBitstreamVera_0.1.1 xfun_0.49
[82] stringi_1.8.4 UCSC.utils_1.2.0 yaml_2.3.10
[85] evaluate_1.0.1 codetools_0.2-20 extrafont_0.19
[88] gdtools_0.4.1 cli_3.6.3 xtable_1.8-4
[91] reticulate_1.40.0 systemfonts_1.1.0 munsell_0.5.1
[94] jquerylib_0.1.4 Rcpp_1.0.13-1 dbplyr_2.5.0
[97] png_0.1-8 parallel_4.4.2 blob_1.2.4
[100] prettyunits_1.2.0 calibrate_1.7.7 viridisLite_0.4.2
[103] crayon_1.5.3 GetoptLong_1.0.5 rlang_1.1.4
[106] KEGGREST_1.46.0 `