MungeSumstats::import_sumstats returned <simpleError in validate_parameters

[shaman-yellow]

I just used the example codes in help(MungeSumstats::find_sumstats):

metagwas <- MungeSumstats::find_sumstats(
  traits = c("parkinson", "alzheimer"),
  min_sample_size = 5000
)
### Only use a subset for testing purposes
ids <- (dplyr::arrange(metagwas, nsnp))$id
datasets <- MungeSumstats::import_sumstats(ids = ids[1])

Everything may downloaded successfully, but got <simpleError...>.

Processing 1 datasets from Open GWAS.

========== Processing dataset : ieu-a-298 ==========

Using previously downloaded VCF.
Formatted summary statistics will be saved to ==>  /tmp/Rtmp0gSh3N/ieu-a-298/ieu-a-298.tsv.gz
Install 'SNPlocs.Hsapiens.dbSNP155.GRCh37' to use 'GRCh37' as 'ref_genome' and 155 as dbSNP version
Done with all processing in 0 minutes.

> datasets
$`ieu-a-298`
<simpleError in validate_parameters(path = path, ref_genome = ref_genome, convert_ref_genome = convert_ref_genome,
     convert_small_p = convert_small_p, es_is_beta = es_is_beta,     compute_z = compute_z, compute_n = compute_n,
 convert_n_int = convert_n_int,     analysis_trait = analysis_trait, INFO_filter = INFO_filter,     FRQ_filter = F
RQ_filter, pos_se = pos_se, effect_columns_nonzero = effect_columns_nonzero,     N_std = N_std, N_dropNA = N_dropN
A, chr_style = chr_style,     rmv_chr = rmv_chr, on_ref_genome = on_ref_genome, infer_eff_direction = infer_eff_di
rection,     eff_on_minor_alleles = eff_on_minor_alleles, strand_ambig_filter = strand_ambig_filter,     allele_fl
ip_check = allele_flip_check, allele_flip_drop = allele_flip_drop,     allele_flip_z = allele_flip_z, allele_flip_
frq = allele_flip_frq,     bi_allelic_filter = bi_allelic_filter, flip_frq_as_biallelic = flip_frq_as_biallelic,  
   snp_ids_are_rs_ids = snp_ids_are_rs_ids, remove_multi_rs_snp = remove_multi_rs_snp,     frq_is_maf = frq_is_maf
, indels = indels, drop_indels = drop_indels,     dbSNP = dbSNP, check_dups = check_dups, write_vcf = write_vcf,  
   return_format = return_format, ldsc_format = ldsc_format,     save_format = save_format, imputation_ind = imput
ation_ind,     log_folder_ind = log_folder_ind, log_mungesumstats_msgs = log_mungesumstats_msgs,     mapping_file 
= mapping_file, tabix_index = tabix_index, chain_source = chain_source,     local_chain = local_chain, drop_na_col
s = drop_na_cols, rmv_chrPrefix = rmv_chrPrefix): Install 'SNPlocs.Hsapiens.dbSNP155.GRCh37' to use 'GRCh37' as 'r
ef_genome' and 155 as dbSNP version>

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Pop!_OS 22.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

time zone: Asia/Shanghai
tzcode source: system (glibc)

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

other attached packages:
[1] utils.tool_0.0.0.9000 nvimcom_0.9-146      

loaded via a namespace (and not attached):
  [1] jsonlite_1.8.9                              magrittr_2.0.3                             
  [3] GenomicFeatures_1.58.0                      farver_2.1.2                               
  [5] BiocIO_1.16.0                               zlibbioc_1.52.0                            
  [7] ragg_1.3.3                                  vctrs_0.6.5                                
  [9] BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1 memoise_2.0.1                              
 [11] Rsamtools_2.22.0                            RCurl_1.98-1.16                            
 [13] askpass_1.2.1                               S4Arrays_1.6.0                             
 [15] curl_6.0.1                                  SparseArray_1.6.0                          
 [17] desc_1.4.3                                  testthat_3.2.1.1                           
 [19] cachem_1.1.0                                ieugwasr_1.0.1                             
 [21] uuid_1.2-1                                  GenomicAlignments_1.42.0                   
 [23] igraph_2.1.1                                lifecycle_1.0.4                            
 [25] pkgconfig_2.0.3                             Matrix_1.7-1                               
 [27] R6_2.5.1                                    fastmap_1.2.0                              
 [29] GenomeInfoDbData_1.2.13                     MatrixGenerics_1.18.0                      
 [31] rsvg_2.6.1                                  colorspace_2.1-1                           
 [33] AnnotationDbi_1.68.0                        S4Vectors_0.44.0                           
 [35] rprojroot_2.0.4                             pkgload_1.4.0                              
 [37] textshaping_0.4.0                           GenomicRanges_1.58.0                       
 [39] RSQLite_2.3.7                               fansi_1.0.6                                
 [41] httr_1.4.7                                  polyclip_1.10-7                            
 [43] abind_1.4-8                                 compiler_4.4.2                             
 [45] remotes_2.5.0                               bit64_4.5.2                                
 [47] withr_3.0.2                                 BiocParallel_1.40.0                        
 [49] viridis_0.6.5                               DBI_1.2.3                                  
 [51] plink2R_1.1                                 pkgbuild_1.4.5                             
 [53] ggforce_0.4.2                               R.utils_2.12.3                             
 [55] MASS_7.3-61                                 openssl_2.2.2                              
 [57] DelayedArray_0.32.0                         rjson_0.2.23                               
 [59] ggsci_3.2.0                                 tools_4.4.2                                
 [61] zip_2.3.1                                   R.oo_1.27.0                                
 [63] glue_1.8.0                                  restfulr_0.0.15                            
 [65] BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000      generics_0.1.3                             
 [67] gtable_0.3.6                                BSgenome_1.74.0                            
 [69] R.methodsS3_1.8.2                           tidyr_1.3.1                                
 [71] data.table_1.16.2                           tidygraph_1.3.1                            
 [73] xml2_1.3.6                                  utf8_1.2.4                                 
 [75] XVector_0.46.0                              BiocGenerics_0.52.0                        
 [77] ggrepel_0.9.6                               pillar_1.9.0                               
 [79] stringr_1.5.1                               later_1.3.2                                
 [81] dplyr_1.1.4                                 tweenr_2.0.3                               
 [83] lattice_0.22-5                              rtracklayer_1.66.0                         
 [85] bit_4.5.0                                   MungeSumstats_1.15.12                      
 [87] tidyselect_1.2.1                            Biostrings_2.74.0                          
 [89] gridExtra_2.3                               IRanges_2.40.0                             
 [91] SummarizedExperiment_1.36.0                 stats4_4.4.2                               
 [93] graphlayouts_1.2.0                          Biobase_2.66.0                             
 [95] brio_1.1.5                                  matrixStats_1.4.1                          
 [97] stringi_1.8.4                               UCSC.utils_1.2.0                           
 [99] yaml_2.3.10                                 codetools_0.2-19                           
 [ reached getOption("max.print") -- omitted 24 entries ]

[Al-Murphy]

Hi! The issue is mentioned in the text output:

Install 'SNPlocs.Hsapiens.dbSNP155.GRCh37' to use 'GRCh37' as 'ref_genome' and 155 as dbSNP version

Install SNPlocs.Hsapiens.dbSNP155.GRCh37 (and likely SNPlocs.Hsapiens.dbSNP155.GRCh38) reference datasets from bioconductor to run mungesumstats. These are only suggested packages rather than dependencies due to their size.

Alan.

[Al-Murphy]

Also note since I'm not sure what version of MSS you are using that IEU GWAS, where the function find_sumstats() gets its data, changed its API so the MSS function would no longer work. The code in MSS was updated in the dev version (>=v1.15.3) and is working there, you can install that from Bioc Dev or straight from github (devtools::install_github("al-murphy/mungesumstats")). See more on this here: #199