Conditional SNP error

[vermaa1]

1. Bug description

finemap_loci() errors out with conditioned_snps must have a length equal to 1 or the number of loci

2. Reproducible example

Code

columnnames<-echodata::construct_colmap(
       munged = FALSE,
       CHR = "chrom",
       POS = "pos",
       SNP = "rsid",
       P = "pval",
       Effect = "beta",
       StdErr = "sebeta",
       Freq = "af",
       MAF = "maf",
       A1 = "ref",
       A2 = "alt",
       N_cases = "num_cases.META",
       N_controls = "num_controls.META",
       proportion_cases = "calculate",
       N = "num_samples.META",
       verbose = TRUE
     )

fullSS_path_file<-"summary.txt.gz"

finemap_loci(
       loci = c("TCF7L2"),
       fullSS_path=fullSS_path_file,
       #data_gene,
       fullSS_genome_build = "hg19",
       results_dir = file.path(tempdir(), "results"),
       dataset_name = "dataset_name",
       dataset_type = "GWAS",
       topSNPs = top_snps_1,
       force_new_subset = TRUE,
       force_new_LD = FALSE,
       force_new_finemap = TRUE,
       finemap_methods = c("ABF", "FINEMAP", "SUSIE"),
       finemap_args = NULL,
       n_causal = 5,
       credset_thresh = 0.95,
       consensus_thresh = 2,
       fillNA = 0,
       conditioned_snps = "auto",
       priors_col = NULL,
       munged = FALSE,
       colmap = columnnames,
       compute_n = "ldsc",
       LD_reference = "1KGphase3",
       LD_genome_build = "hg19",
       leadSNP_LD_block = FALSE,
       superpopulation = "EUR",
       download_method = "axel",
       bp_distance = 5e+05,
       min_POS = NA,
       max_POS = NA,
       min_MAF = NA,
       trim_gene_limits = FALSE,
       max_snps = NULL,
       min_r2 = 0,
       remove_variants = FALSE,
       remove_correlates = FALSE,
       query_by = "tabix",
       case_control = TRUE,
       qtl_suffixes = NULL,
      
       return_all = TRUE,
       use_tryCatch = TRUE,
       seed = 2022,
       nThread = 1,
       verbose = TRUE)

Console output

┌──────────────────────────────────────────┐                                                                                                                   │·······················································
│                                          │                                                                                                                   │·······················································
│   )))> 🦇 TCF7L2 [locus 1 / 1] 🦇 <(((   │                                                                                                                   │·······················································
│                                          │                                                                                                                   │·······················································
└──────────────────────────────────────────┘                                                                                                                   │·······················································
conditioned_snps must have a length equal to 1 or the number of lociLocus TCF7L2 complete in: 0 min                                                            │·······················································
                                                                                                                                                               │·······················································
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────│·······················································
                                                                                                                                                               │·······················································
── Step 6 ▶▶▶ Postprocess data 🎁 ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────│·······················································
                                                                                                                                                               │·······················································
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────│·······················································
Returning results as nested list.                                                                                                                              │·······················································
All loci done in: 0 min                                                                                                                                        │·······················································
$TCF7L2                                                                                                                                                        │·······················································
NULL                                                                                                                                                           │·······················································
                                                                                                                                                               │·······················································
$merged_dat                                                                                                                                                    │·······················································
Null data.table (0 rows and 0 cols)  

Data

Header of lead SNP dataframe

head(top_snp_1)

    Locus   Gene CHR        BP        SNP             P  Effect                                                                                                │·······················································
1: TCF7L2 TCF7L2  10 112994312 rs34872471 9.881313e-24 -0.2316                                                                                                │·······················································
2: TCF7L2 TCF7L2  10 112990398 rs11196182  5.800000e-18  0.1347 

3. Session info

(Add output of the R function utils::sessionInfo() below. This helps us assess version/OS conflicts which could be causing bugs.)

> utils::sessionInfo()                                                                                                                                         │···························
R version 4.1.3 (2022-03-10)                                                                                                                                   │···························
Platform: x86_64-conda-linux-gnu (64-bit)                                                                                                                      │···························
Running under: Red Hat Enterprise Linux 8.6 (Ootpa)                                                                                                            │···························
                                                                                                                                                               │···························
Matrix products: default                                                                                                                                       │···························
BLAS/LAPACK: /autofs/nccs-svm1_home1/anuragv/.conda/envs/echoverse/lib/libopenblasp-r0.3.21.so                                                                 │···························
                                                                                                                                                               │···························
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                                                                                                            │···························
                                                                                                                                                               │···························
attached base packages:                                                                                                                                        │···························
[1] stats4    stats     graphics  grDevices utils     datasets  methods                                                                                        │···························
[8] base                                                                                                                                                       │···························
                                                                                                                                                               │···························
other attached packages:                                                                                                                                       │···························
 [1] BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1                                                                                                               │···························
 [2] SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20                                                                                                                  │···························
 [3] BSgenome_1.62.0                                                                                                                                           │···························
 [4] rtracklayer_1.54.0                                                                                                                                        │···························
 [5] Biostrings_2.62.0                                                                                                                                         │···························
 [6] XVector_0.34.0                                                                                                                                            │···························
 [7] GenomicRanges_1.46.1                                                                                                                                      │···························
 [8] GenomeInfoDb_1.30.1                                                                                                                                       │·······················································
 [9] IRanges_2.28.0                                                                                                                                            │·······················································
[10] S4Vectors_0.32.4                                                                                                                                          │·······················································
[11] BiocGenerics_0.40.0                                                                                                                                       │·······················································
[12] echolocatoR_2.0.1                                                                                                                                         │·······················································
[13] data.table_1.14.4                                                                                                                                         │·······················································
[14] forcats_0.5.2                                                                                                                                             │·······················································
[15] stringr_1.4.1                                                                                                                                             │·······················································
[16] dplyr_1.0.10                                                                                                                                                       
 [31] dbplyr_2.2.1                readxl_1.4.1                                                                                                         [0/1811]│···························
 [33] Rgraphviz_2.38.0            igraph_1.3.5                                                                                                                 │···························
 [35] DBI_1.1.3                   htmlwidgets_1.5.4                                                                                                            │···························
 [37] reshape_0.8.9               downloadR_0.99.4                                                                                                             │···························
 [39] googledrive_2.0.0           ellipsis_0.3.2                                                                                                               │···························
 [41] backports_1.4.1             biomaRt_2.50.3                                                                                                               │···························
 [43] deldir_1.0-6                MatrixGenerics_1.6.0                                                                                                         │···························
 [45] MungeSumstats_1.2.4         vctrs_0.4.2                                                                                                                  │···························
 [47] Biobase_2.54.0              ensembldb_2.18.4                                                                                                             │···························
 [49] cachem_1.0.6                withr_2.5.0                                                                                                                  │···························
 [51] checkmate_2.1.0             vroom_1.6.0                                                                                                                  │···························
 [53] GenomicAlignments_1.30.0    prettyunits_1.1.1                                                                                                            │···························
 [55] cluster_2.1.4               ape_5.6-2                                                                                                                    │···························
 [57] dir.expiry_1.2.0            lazyeval_0.2.2                                                                                                               │···························
 [59] crayon_1.5.2                basilisk.utils_1.6.0                                                                                                         │···························
 [61] crul_1.3                    pkgconfig_2.0.3                                                                                                              │···························
 [63] nlme_3.1-160                ProtGenerics_1.26.0                                                                                                          │···························
 [65] XGR_1.1.8                   nnet_7.3-18                                                                                                                  │···························
 [67] gitcreds_0.1.2              rlang_1.0.6                                                                                                                  │···························
 [69] lifecycle_1.0.3             filelock_1.0.2                                                                                                               │···························
 [71] httpcode_0.3.0              BiocFileCache_2.2.1                                                                                                          │···························
 [73] modelr_0.1.9                echotabix_0.99.8                                                                                                             │···························
 [75] dichromat_2.0-0.1           cellranger_1.1.0                                                                                                             │···························
 [77] coloc_5.1.0.1               matrixStats_0.62.0                                                                                                           │···························
 [79] graph_1.72.0                Matrix_1.5-1                                                                                                                 │···························
 [81] osfr_0.2.9                  boot_1.3-28                                                                                                                  │···························
 [83] reprex_2.0.2                base64enc_0.1-3                                                                                                              │···························
 [85] googlesheets4_1.0.1         png_0.1-7                                                                                                                    │···························
 [87] viridisLite_0.4.1           rjson_0.2.21                                                                                                                 │···························
 [89] rootSolve_1.8.2.3           bitops_1.0-7                                                                                                                 │···························
 [91] R.oo_1.25.0                 ggnetwork_0.5.10                                                                                                             │···························
 [93] blob_1.2.3                  mixsqp_0.3-43                                                                                                                │···························
 [95] echoplot_0.99.5             dnet_1.1.7                                                                                                                   │···························
 [97] jpeg_0.1-9                  echodata_0.99.14                                                                                                             │···························
 [99] scales_1.2.1                memoise_2.0.1                                                                                                                │·······················································
[101] magrittr_2.0.3              plyr_1.8.7                                                                                                                   │·······················································
[103] hexbin_1.28.2               zlibbioc_1.40.0                                                                                                              │·······················································
[105] compiler_4.1.3              echoconda_0.99.7                                                                                                             │·······················································
[107] BiocIO_1.4.0                RColorBrewer_1.1-3                                                                                                           │·······················································
[109] catalogueR_1.0.0            Rsamtools_2.10.0                                                                                                             │·······················································
[111] cli_3.4.1                   echoannot_0.99.7                                                                                                             │·······················································
[113] patchwork_1.1.2             htmlTable_2.4.1                                                                                                              │·······················································
[115] Formula_1.2-4               MASS_7.3-58.1                                                                                                                │·······················································
[117] tidyselect_1.2.0            stringi_1.7.8                                                                                                                │·······················································
[119] yaml_2.3.5                  supraHex_1.32.0                                                                                                              │·······················································
[121] latticeExtra_0.6-30         ggrepel_0.9.1                                                                                                                │·······················································
[123] grid_4.1.3                  VariantAnnotation_1.40.0                                                                                                     │·······················································
[125] tools_4.1.3                 lmom_2.9                                                                                                                     │·······················································
[127] parallel_4.1.3              rstudioapi_0.14                                                                                                              │·······················································
[129] foreign_0.8-83              piggyback_0.1.4                                                                                                              │·······················································
[131] gridExtra_2.3               gld_2.6.5                                                                                                                    │·······················································
[133] digest_0.6.29               snpStats_1.44.0                                                                                                              │·······················································
[135] BiocManager_1.30.18         Rcpp_1.0.9                                                                                                                   │·······················································
[137] broom_1.0.1                 OrganismDbi_1.36.0                                                                                                           │·······················································
[139] httr_1.4.4                  AnnotationDbi_1.56.2                                                                                                         │·······················································
[141] RCircos_1.2.2               ggbio_1.42.0                                                                                                                 │·······················································
[143] biovizBase_1.42.0           colorspace_2.0-3                                                                                                             │·······················································
[145] rvest_1.0.3                 XML_3.99-0.11                                                                                                                │·······················································
[147] fs_1.5.2                    reticulate_1.26                                                                                                              │·······················································
[149] splines_4.1.3               RBGL_1.70.0                                                                                                                  │·······················································
[151] expm_0.999-6                gh_1.3.1                                                                                                                     │·······················································
[153] echofinemap_0.99.3          basilisk_1.6.0                                                                                                               │·······················································
[155] Exact_3.2                   jsonlite_1.8.2                                                                                                               │·······················································
[157] susieR_0.12.27              R6_2.5.1                                                                                                                     │·······················································
[159] Hmisc_4.7-1                 pillar_1.8.1                                                                                                                 │·······················································
[161] htmltools_0.5.3             glue_1.6.2                                                                                                                   │·······················································
[163] fastmap_1.1.0               DT_0.25                                                                                                                      │·······················································
[165] BiocParallel_1.28.3         class_7.3-20                                                                                                                 │·······················································
[167] mvtnorm_1.1-3               utf8_1.2.2                                                                                                                   │·······················································
[169] lattice_0.20-45             curl_4.3.3                                                                                                                   │·······················································
[171] DescTools_0.99.46           zip_2.2.1                                                                                                                    │·······················································
[173] openxlsx_4.2.5              interp_1.1-3                                                                                                                 │·······················································
[175] survival_3.4-0              googleAuthR_2.0.0                                                                                                            │·······················································
[177] munsell_0.5.0               e1071_1.7-11                                                                                                                 │·······················································
[179] GenomeInfoDbData_1.2.7      haven_2.5.1                                                                                                                  │·······················································
[181] reshape2_1.4.4              gtable_0.3.1      

[vermaa1]

Please let me know if you need other details to troubleshoot the issue.

[vermaa1]

@bschilder - Do you have any recommendations on how to resolve this issue?

[bschilder]

haven't had a chance to look work on this project for a while but will let you know when i do

[bschilder]

Hi @vermaa1, sorry for the delay, finally have some time to look at this now.

It looks like you may have sent just a portion of the console output. Would you mind sending the full output?
Actually, I think it's just abbreviated bc it exited early.

[bschilder]

Ok, actually I think I see what's happening here. The conditioned SNPs are being extracted automatically from the topSNPs dataframe, which contains multiple rows for the same locus. However you specify to finemap only one locus (loci = c("TCF7L2") so there's a mismatch between the number of proposed conditioned SNPs and the number of loci actually being analyzed. But in practice, users should be able to specify however many conditioned SNPs they want per Locus.

I've just added some more flexible handling of conditioned SNPs (with warning messages about how conditioned_snps will be used) to avoid this. If you reinstall, and rerun can you let me know if this works for you?

[vermaa1]

Okay. I will give it a try.

[bschilder]

Did this work for you @vermaa1 ?