JonnyBaseball
commented
1 year ago BUG DESCRIPTION (SUPPLEMENT TO ISSUE)
I was also unable to install Polyfun module with your example data and here I responded 'y' to prompt to install:
REPRODUCIBLE EXAMPLE
topSNPs <- echodata::import_topSNPs(
- topSS = echodata::topSNPs_Nalls2019_raw,
- colmap = colmap,
- grouping_vars = "Locus Number")
- Constructing locus names from CHR and index SNP.
Standardising column headers.
First line of summary statistics file:
SNP CHR BP Nearest Gene QTL Nominated Gene (nearest QTL) Effect allele Other allele Effect allele frequency Beta, all studies SE, all studies P, all studies P, COJO, all studies P, random effects, all studies P, Conditional 23AndMe only P, 23AndMe only I2, all studies Freq1, previous studies Beta, previous studies StdErr, previous studies P, previous studies I2, previous studies Freq1, new studies Beta, new studies StdErr, new studies P, new studies I2, new studies Passes pooled 23andMe QC Known GWAS locus within 1MB Failed final filtering and QC Locus within 250KB Locus Number Locus Gene
Returning unmapped column names without making them uppercase. - Mapping colnames from MungeSumstats ==> echolocatoR
fullSS_path <- echodata::example_fullSS(dataset = "Nalls2019") Writing file to ==> /var/folders/rl/6vqvm_h5319fml5s4vw8fbfr0000gn/T//RtmpNSorp8/nalls2019.fullSS_subset.tsv
results <- echolocatoR::finemap_loci(
- fullSS_path = fullSS_path,
- topSNPs = topSNPs,
- loci = c("BST1"),
- LD_reference = "1KGphase3",
dataset_name = "Nalls23andMe_2019",
- fullSS_genome_build = "hg19",
- bp_distance = 1000,
- finemap_methods = c("ABF","SUSIE","FINEMAP","POLYFUN_FINEMAP","POLYFUN_SUSIE","PAINTOR","COJO_conditional","COJO_joint","COJO_stepwise"),
- munged = TRUE)
CONSOLE OUTPUT
PolyFun is not installed. Reinstall echofinemap with PolyFun? This will automatically restart R. (y/n): y
Installing PolyFun submodule.
Cloning into '/var/folders/rl/6vqvm_h5319fml5s4vw8fbfr0000gn/T//RtmpNSorp8/file9c3057a3dc73'...
fatal: unable to access 'https://github.com/RajLabMSSM/echofinemap/': Could not resolve host: github.com
Error in package_file():
! '/var/folders/rl/6vqvm_h5319fml5s4vw8fbfr0000gn/T//RtmpNSorp8/file9c3057a3dc73' is not a directory.
Run rlang::last_error() to see where the error occurred.
rlang::last_error() <error/rlang_error> Error in
package_file(): ! '/var/folders/rl/6vqvm_h5319fml5s4vw8fbfr0000gn/T//RtmpNSorp8/file9c3057a3dc73' is not a directory.Backtrace:
- echolocatoR::finemap_loci(...)
- echofinemap::POLYFUN_install()
- echofinemap:::install_submodule_git("https://github.com/RajLabMSSM/echofinemap")
- devtools::install(install_dir, ...)
- devtools::as.package(pkg)
- devtools::package_file(path = x) Run
rlang::last_trace()to see the full context.
BUG DESCRIPTION As well, I was unable to access PAINTOR
REPRODUCIBLE EXAMPLE
results <- echolocatoR::finemap_loci(
- fullSS_path = fullSS_path,
- topSNPs = topSNPs,
- loci = c("BST1"),
- LD_reference = "1KGphase3",
dataset_name = "Nalls23andMe_2019",
- fullSS_genome_build = "hg19",
- bp_distance = 1000,
- finemap_methods = c("ABF","SUSIE","FINEMAP","PAINTOR","COJO_conditional","COJO_joint","COJO_stepwise"),
- munged = TRUE)
CONSOLE OUTPUT
Error in PAINTOR_find_executable(paintor_path = paintor_path) : PAINTOR executable cannot be found.
SESSION INFO
utils::sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7
Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] forestploter_0.2.3 snpStats_1.48.0 Matrix_1.5-3 survival_3.4-0 readr_2.1.3 GenomeInfoDb_1.34.3 IRanges_2.32.0
[8] S4Vectors_0.36.0 BiocGenerics_0.44.0 echolocatoR_2.0.3
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 rtracklayer_1.58.0 GGally_2.1.2
[4] R.methodsS3_1.8.2 ragg_1.2.4 tidyr_1.2.1
[7] echoLD_0.99.8 ggplot2_3.4.0 bit64_4.0.5
[10] knitr_1.41 irlba_2.3.5.1 DelayedArray_0.24.0
[13] R.utils_2.12.2 data.table_1.14.6 rpart_4.1.19
[16] KEGGREST_1.38.0 RCurl_1.98-1.9 AnnotationFilter_1.22.0
[19] generics_0.1.3 GenomicFeatures_1.50.2 callr_3.7.3
[22] usethis_2.1.6 RSQLite_2.2.19 proxy_0.4-27
[25] bit_4.0.5 tzdb_0.3.0 httpuv_1.6.6
[28] xml2_1.3.3 SummarizedExperiment_1.28.0 assertthat_0.2.1
[31] viridis_0.6.2 gargle_1.2.1 xfun_0.35
[34] hms_1.1.2 promises_1.2.0.1 fansi_1.0.3
[37] restfulr_0.0.15 progress_1.2.2 dbplyr_2.2.1
[40] readxl_1.4.1 Rgraphviz_2.42.0 igraph_1.3.5
[43] DBI_1.1.3 htmlwidgets_1.5.4 reshape_0.8.9
[46] downloadR_0.99.5 purrr_0.3.5 ellipsis_0.3.2
[49] dplyr_1.0.10 ggnewscale_0.4.8 backports_1.4.1
[52] biomaRt_2.54.0 deldir_1.0-6 MatrixGenerics_1.10.0
[55] MungeSumstats_1.7.2 vctrs_0.5.1 Biobase_2.58.0
[58] remotes_2.4.2 ensembldb_2.22.0 cachem_1.0.6
[61] withr_2.5.0 BSgenome_1.66.1 checkmate_2.1.0
[64] vroom_1.6.0 GenomicAlignments_1.34.0 prettyunits_1.1.1
[67] cluster_2.1.4 ape_5.6-2 dir.expiry_1.6.0
[70] lazyeval_0.2.2 crayon_1.5.2 basilisk.utils_1.10.0
[73] crul_1.3 pkgconfig_2.0.3 labeling_0.4.2
[76] pkgload_1.3.2 nlme_3.1-160 ProtGenerics_1.30.0
[79] XGR_1.1.8 devtools_2.4.5 nnet_7.3-18
[82] pals_1.7 rlang_1.0.6 miniUI_0.1.1.1
[85] lifecycle_1.0.3 filelock_1.0.2 httpcode_0.3.0
[88] BiocFileCache_2.6.0 echotabix_0.99.8 dichromat_2.0-0.1
[91] cellranger_1.1.0 coloc_5.1.0.1 matrixStats_0.63.0
[94] graph_1.76.0 osfr_0.2.9 boot_1.3-28.1
[97] base64enc_0.1-3 processx_3.8.0 png_0.1-8
[100] viridisLite_0.4.1 rjson_0.2.21 rootSolve_1.8.2.3
[103] bitops_1.0-7 R.oo_1.25.0 ggnetwork_0.5.10
[106] Biostrings_2.66.0 blob_1.2.3 mixsqp_0.3-48
[109] stringr_1.4.1 echoplot_0.99.6 dnet_1.1.7
[112] jpeg_0.1-9 echodata_0.99.16 BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1
[115] scales_1.2.1 memoise_2.0.1 magrittr_2.0.3
[118] plyr_1.8.8 hexbin_1.28.2 zlibbioc_1.44.0
[121] compiler_4.2.0 echoconda_0.99.8 BiocIO_1.8.0
[124] RColorBrewer_1.1-3 catalogueR_1.0.0 EnsDb.Hsapiens.v75_2.99.0
[127] Rsamtools_2.14.0 cli_3.4.1 urlchecker_1.0.1
[130] XVector_0.38.0 echoannot_0.99.10 ps_1.7.2
[133] patchwork_1.1.2 htmlTable_2.4.1 Formula_1.2-4
[136] MASS_7.3-58.1 tidyselect_1.2.0 stringi_1.7.8
[139] textshaping_0.3.6 yaml_2.3.6 supraHex_1.36.0
[142] latticeExtra_0.6-30 ggrepel_0.9.2 grid_4.2.0
[145] VariantAnnotation_1.44.0 tools_4.2.0 lmom_2.9
[148] parallel_4.2.0 rstudioapi_0.14 foreign_0.8-83
[151] piggyback_0.1.4 gridExtra_2.3 gld_2.6.6
[154] farver_2.1.1 RcppZiggurat_0.1.6 digest_0.6.30
[157] BiocManager_1.30.19 shiny_1.7.3 Rcpp_1.0.9
[160] GenomicRanges_1.50.1 later_1.3.0 OrganismDbi_1.40.0
[163] httr_1.4.4 AnnotationDbi_1.60.0 RCircos_1.2.2
[166] ggbio_1.46.0 biovizBase_1.46.0 colorspace_2.0-3
[169] XML_3.99-0.12 fs_1.5.2 reticulate_1.26
[172] splines_4.2.0 RBGL_1.74.0 expm_0.999-6
[175] echofinemap_0.99.4 basilisk_1.10.2 Exact_3.2
[178] mapproj_1.2.9 SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.22 sessioninfo_1.2.2
[181] systemfonts_1.0.4 xtable_1.8-4 jsonlite_1.8.3
[184] Rfast_2.0.6 susieR_0.12.27 R6_2.5.1
[187] profvis_0.3.7 Hmisc_4.7-2 mime_0.12
[190] pillar_1.8.1 htmltools_0.5.3 glue_1.6.2
[193] fastmap_1.1.0 DT_0.26 BiocParallel_1.32.3
[196] class_7.3-20 codetools_0.2-18 maps_3.4.1
[199] pkgbuild_1.4.0 mvtnorm_1.1-3 utf8_1.2.2
[202] lattice_0.20-45 tibble_3.1.8 curl_4.3.3
[205] DescTools_0.99.47 zip_2.2.2 openxlsx_4.2.5.1
[208] interp_1.1-3 googleAuthR_2.0.0 munsell_0.5.0
[211] e1071_1.7-12 GenomeInfoDbData_1.2.9 reshape2_1.4.4
[214] gtable_0.3.1
2022-12-06 12:40:35.793 R[39984:29884093] -deltaZ is deprecated for NSEventTypeMagnify. Please use -magnification.
1. Bug description
PolyFun is not installed. Reinstall echofinemap with PolyFun? This will automatically restart R. (y/n): Error in echofinemap::POLYFUN_install() : PolyFun is not installed.
Awesome package! Also thanks in advance for any help you can give me!
Expected behaviour
Your example echodata::BCST results included POLYFUN_SUSIE results.
2. Reproducible example
results <- echolocatoR::finemap_loci(
dataset_name = "cf.longevity",
Console output
PolyFun is not installed. Reinstall echofinemap with PolyFun? This will automatically restart R. (y/n): Error in echofinemap::POLYFUN_install() : PolyFun is not installed.
Data
As set forth in the next comment, I tried to access Polyfun using your example data. There I also responded 'y' to option to install Polyfun.
If it would help to see my data, I can certainly upload a small sample. Note that there was no problem when I cut out all but "ABF" (not relevant since not binary), "SUSIE", and "FINEMAP". I used a GWAS generated using GSEM (with 6.7 million snps, munged down using MungeSumstats to 3.7 million due to multiallelic snps).
(If possible, upload a small sample of your data so that we can reproduce the bug on our end. If that's not possible, please at least include a screenshot of your data and other relevant details.)
3. Session info
(Add output of the R function
utils::sessionInfo()below. This helps us assess version/OS conflicts which could be causing bugs.)