Nott bug

[AMCalejandro]

1. Bug description

I think there is a bug somewhere trying to plot Nott's epigenetic data.
I guess somewhere I did not manage to find there is a "RUE" instead of a "TRUE"

The code to run finemap_loci

finemap_loci(# GENERAL ARGUMENTS 
  topSNPs = topSNPs,
  results_dir = fullRS_path,
  loci = topSNPs$Locus,
  dataset_name = "PiD_sURVIVAL_NOTT",
  dataset_type = "GWAS",  
  
  
  force_new_subset = TRUE,
  force_new_LD = FALSE,
  force_new_finemap = FALSE,
  remove_tmps = FALSE,
  
  finemap_methods = c("SUSIE"),
  
  # Munge full sumstats first
  munged = FALSE,
  colmap = columnsnames,
  # SUMMARY STATS ARGUMENTS
  fullSS_path = newSS_name_colmap,
  fullSS_genome_build = "hg19",
  query_by ="tabix",
  
  
  bp_distance = 500000*2,
  min_MAF = 0.001, 
  trim_gene_limits = FALSE,
  case_control = TRUE,
  
  # FINE-MAPPING ARGUMENTS
  ## General
  n_causal = 5,
  credset_thresh = .95,
  consensus_thresh = 2,
  
  
  # LD ARGUMENTS 
  LD_reference = "1KGphase3",#"UKB",
  superpopulation = "EUR",
  download_method = "axel",
  LD_genome_build = "hg19",
  leadSNP_LD_block = FALSE,
  
  #### PLotting args ####
  plot_types = c("fancy"),
  show_plot = TRUE,
  zoom = c("1x", "3x", "4x", "5x" ,"6x", "7x", "8x", "20x"),
  #zoom = "1x",
  tx_biotypes = NULL,
  nott_epigenome = TRUE,
  nott_show_placseq = TRUE,
  nott_binwidth = 200,
  nott_bigwig_dir = NULL,
  #xgr_libnames =c("ENCODE_TFBS_ClusteredV3_CellTypes", "TFBS_Conserved", "Uniform_TFBS"),
  
  
  
  #### General args ####
  seed = 2022,
  nThread = 20,
  verbose = TRUE
)

The output (only the part of the plotting)

────────────────────────────────────────────────────────────────────────────────

── Step 5 ▶▶▶ Plot 📈 ──────────────────────────────────────────────────────────

────────────────────────────────────────────────────────────────────────────────
+-------- Locus Plot:  CSMD1 --------+
+ support_thresh = 2
+ Calculating mean Posterior Probability (mean.PP)...
+ 1 fine-mapping methods used.
+ 0 Credible Set SNPs identified.
+ 0 Consensus SNPs identified.
+ Filling NAs in CS cols with 0.
+ Filling NAs in PP cols with 0.
LD_matrix detected. Coloring SNPs by LD with lead SNP.
++ echoplot:: GWAS full window track
++ echoplot:: GWAS track
++ echoplot:: Merged fine-mapping track
Melting PP and CS from 2 fine-mapping methods.
+ echoplot:: Constructing SNP labels.
Adding SNP group labels to locus plot.
++ echoplot:: Adding Gene model track.
Converting dat to GRanges object.
max_transcripts= 1 . 
2  transcripts from  2  genes returned.
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Constructing graphics...
NOTT2019:: Creating epigenomic histograms plot
+ Inferring genomic limits for window: 1x
Constructing GRanges query using min/max ranges across one or more chromosomes.
Downloading data from UCSC.
Importing... [1] exvivo_H3K27ac_tbp
Importing... [2] microglia_H3K27ac
Importing... [3] neurons_H3K27ac
Importing... [4] oligodendrocytes_H3K27ac
Importing... [5] astrocytes_H3K27ac
Importing... [6] exvivo_atac_tbp
Importing... [7] microglia_atac
Importing... [8] neurons_atac
Importing... [9] oligodendrocytes_atac
Importing... [10] astrocytes_atac
Importing... [11] microglia_H3K4me3
Importing... [12] neurons_H3K4me3
Importing... [13] oligodendrocytes_H3K4me3
Importing... [14] astrocytes_H3K4me3
Saving bigwig query ==> /tmp/RtmpR6G9c0/CSMD1_Nott2019_bigwig.rds
Importing previously downloaded files: /home/rstudio/.cache/R/echoannot/NOTT2019_epigenomic_peaks.rds
++ NOTT2019:: 634,540 ranges retrieved.
dat is already a GRanges object.
361 query SNP(s) detected with reference overlap.
+ Calculating max histogram height
+ Converting label units to Mb.
NOTT2019:: Creating PLAC-seq interactome plot
++ NOTT2019:: Getting promoter cell-type-specific data.
++ NOTT2019:: Getting interactome data.
++ NOTT2019:: Getting regulatory regions data.
Importing Astrocyte enhancers ...
Importing Astrocyte promoters ...
Importing Neuronal enhancers ...
Importing Neuronal promoters ...
Importing Oligo enhancers ...
Importing Oligo promoters ...
Importing Microglia enhancers ...
Importing Microglia promoters ...
Converting dat to GRanges object.
++ NOTT2019:: Getting interaction anchors data.
Importing Microglia interactome ...
Importing Neuronal interactome ...
Importing Oligo interactome ...
Converting dat to GRanges object.
27 query SNP(s) detected with reference overlap.
Converting dat to GRanges object.
14 query SNP(s) detected with reference overlap.
Converting dat to GRanges object.
Preparing data for highlighting PLAC-seq interactions that overlap with SNP subset: Support>0
No target SNPs overlapped with PLAC-seq anchors.Locus CSMD1 complete in: 5.1 min

────────────────────────────────────────────────────────────────────────────────

── Step 6 ▶▶▶ Postprocess data 🎁 ──────────────────────────────────────────────

────────────────────────────────────────────────────────────────────────────────
Returning results as nested list.
All loci done in: 9.08 min
$NLGN1
NULL

$KATNAL2
NULL

$CSMD1
NULL

$merged_dat
Null data.table (0 rows and 0 cols)

Warning messages:
1: In .Call(.make_vcf_geno, filename, fixed, names(geno), as.list(geno),  :
  converting NULL pointer to R NULL
2: In .local(x, ...) : variants with >1 ALT allele are set to NA
3: In .Call(.make_vcf_geno, filename, fixed, names(geno), as.list(geno),  :
  converting NULL pointer to R NULL
4: In .local(x, ...) : variants with >1 ALT allele are set to NA
5: In .Call(.make_vcf_geno, filename, fixed, names(geno), as.list(geno),  :
  converting NULL pointer to R NULL
6: In .local(x, ...) : variants with >1 ALT allele are set to NA
Error: object 'RUE' not found
Execution halted

SessionInfo

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

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

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

other attached packages:
 [1] snpStats_1.48.0                          Matrix_1.4-1                             survival_3.3-1                           SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.22
 [5] susieR_0.12.28                           SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20 BSgenome_1.66.1                          rtracklayer_1.58.0                      
 [9] Biostrings_2.66.0                        XVector_0.38.0                           GenomicRanges_1.50.1                     GenomeInfoDb_1.34.3                     
[13] IRanges_2.32.0                           S4Vectors_0.36.0                         BiocGenerics_0.44.0                      data.table_1.14.2                       
[17] forcats_0.5.2                            stringr_1.4.1                            dplyr_1.0.10                             purrr_0.3.4                             
[21] readr_2.1.2                              tidyr_1.2.0                              tibble_3.1.8                             ggplot2_3.3.6                           
[25] tidyverse_1.3.2                          reticulate_1.26                          coloc_5.1.0                              echolocatoR_2.0.3                       

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.3              GGally_2.1.2                R.methodsS3_1.8.2           ragg_1.2.2                  echoLD_0.99.8               bit64_4.0.5                
  [7] knitr_1.40                  irlba_2.3.5                 DelayedArray_0.24.0         R.utils_2.12.0              rpart_4.1.16                KEGGREST_1.38.0            
 [13] RCurl_1.98-1.8              AnnotationFilter_1.22.0     generics_0.1.3              GenomicFeatures_1.50.2      RSQLite_2.2.16              proxy_0.4-27               
 [19] bit_4.0.4                   tzdb_0.3.0                  xml2_1.3.3                  lubridate_1.8.0             SummarizedExperiment_1.28.0 assertthat_0.2.1           
 [25] viridis_0.6.2               gargle_1.2.0                xfun_0.32                   hms_1.1.2                   fansi_1.0.3                 restfulr_0.0.15            
 [31] progress_1.2.2              dbplyr_2.2.1                readxl_1.4.1                Rgraphviz_2.41.1            igraph_1.3.4                DBI_1.1.3                  
 [37] htmlwidgets_1.5.4           reshape_0.8.9               downloadR_0.99.5            googledrive_2.0.0           ellipsis_0.3.2              ggnewscale_0.4.7           
 [43] backports_1.4.1             biomaRt_2.54.0              deldir_1.0-6                MatrixGenerics_1.10.0       MungeSumstats_1.7.1         vctrs_0.4.1                
 [49] Biobase_2.58.0              ensembldb_2.22.0            cachem_1.0.6                withr_2.5.0                 checkmate_2.1.0             GenomicAlignments_1.34.0   
 [55] prettyunits_1.1.1           cluster_2.1.3               ape_5.6-2                   dir.expiry_1.6.0            lazyeval_0.2.2              crayon_1.5.1               
 [61] basilisk.utils_1.10.0       crul_1.2.0                  labeling_0.4.2              pkgconfig_2.0.3             nlme_3.1-159                ProtGenerics_1.30.0        
 [67] XGR_1.1.8                   nnet_7.3-17                 pals_1.7                    rlang_1.0.5                 lifecycle_1.0.1             filelock_1.0.2             
 [73] httpcode_0.3.0              BiocFileCache_2.6.0         modelr_0.1.9                echotabix_0.99.8            dichromat_2.0-0.1           cellranger_1.1.0           
 [79] matrixStats_0.62.0          graph_1.76.0                osfr_0.2.8                  boot_1.3-28                 reprex_2.0.2                base64enc_0.1-3            
 [85] googlesheets4_1.0.1         png_0.1-7                   viridisLite_0.4.1           rjson_0.2.21                rootSolve_1.8.2.3           bitops_1.0-7               
 [91] R.oo_1.25.0                 ggnetwork_0.5.10            blob_1.2.3                  mixsqp_0.3-43               echoplot_0.99.6             dnet_1.1.7                 
 [97] jpeg_0.1-9                  echodata_0.99.16            scales_1.2.1                memoise_2.0.1               magrittr_2.0.3              plyr_1.8.7                 
[103] hexbin_1.28.2               zlibbioc_1.44.0             compiler_4.2.0              echoconda_0.99.8            BiocIO_1.8.0                RColorBrewer_1.1-3         
[109] catalogueR_1.0.0            EnsDb.Hsapiens.v75_2.99.0   Rsamtools_2.14.0            cli_3.3.0                   echoannot_0.99.10           patchwork_1.1.2            
[115] htmlTable_2.4.1             Formula_1.2-4               MASS_7.3-58.1               tidyselect_1.1.2            stringi_1.7.8               textshaping_0.3.6          
[121] yaml_2.3.5                  supraHex_1.35.0             latticeExtra_0.6-30         ggrepel_0.9.1               grid_4.2.0                  VariantAnnotation_1.44.0   
[127] tools_4.2.0                 lmom_2.9                    parallel_4.2.0              rstudioapi_0.14             foreign_0.8-82              piggyback_0.1.3            
[133] gridExtra_2.3               gld_2.6.5                   farver_2.1.1                RcppZiggurat_0.1.6          digest_0.6.29               BiocManager_1.30.18        
[139] Rcpp_1.0.9                  broom_1.0.1                 OrganismDbi_1.40.0          httr_1.4.4                  AnnotationDbi_1.60.0        RCircos_1.2.2              
[145] ggbio_1.46.0                biovizBase_1.46.0           colorspace_2.0-3            rvest_1.0.3                 XML_3.99-0.10               fs_1.5.2                   
[151] splines_4.2.0               RBGL_1.74.0                 expm_0.999-6                echofinemap_0.99.4          basilisk_1.9.12             Exact_3.1                  
[157] mapproj_1.2.8               systemfonts_1.0.4           jsonlite_1.8.0              Rfast_2.0.6                 R6_2.5.1                    Hmisc_4.7-1                
[163] pillar_1.8.1                htmltools_0.5.3             glue_1.6.2                  fastmap_1.1.0               DT_0.24                     BiocParallel_1.32.1        
[169] class_7.3-20                codetools_0.2-18            maps_3.4.0                  mvtnorm_1.1-3               utf8_1.2.2                  lattice_0.20-45            
[175] curl_4.3.2                  DescTools_0.99.46           zip_2.2.0                   openxlsx_4.2.5              interp_1.1-3                googleAuthR_2.0.0