MotifScan fails when there is a gene with more than one motif

[jmodlis]

Thank you for your development of this package! I'm running into an issue when using MotifScan with EnsDb.Mmusculus.v79 and mm10. I get the the error message below.

Error message

> [1] "Matching motifs..."
> [1] "Getting putative TF target genes..."
> Error in `$<-.data.frame`(`*tmp*`, "n_targets", value = c(Arnt = 5672L,  : 
>  replacement has 828 rows, data has 879

Stepping through the source code line by line, I find that the error is
triggered in the last line in the block of code below.

  colnames(tf_match) <- motif_df$motif_name ###

    # only keep genes that are in the Seurat object and in the given EnsDb:
    gene_list <- rownames(seurat_obj)
    gene_list <- gene_list[gene_list %in% rownames(tf_match)]
    tf_match <- tf_match[gene_list,]

    # get list of target genes for each TF:
    print('Getting putative TF target genes...')
    tfs <- motif_df$motif_name ###
    tf_targets <- list()
    n_targets <- list()
    for(cur_tf in tfs){      tf_targets[[cur_tf]] <- names(tf_match[,cur_tf][tf_match[,cur_tf]])
        n_targets[[cur_tf]] <- length(tf_targets[[cur_tf]] )
    }
    n_targets <- unlist(n_targets)

    # add number of target genes to motif_df
    motif_df$n_targets <- n_targets

The error is occurring because there are some genes that have more than
one motif ID. In other words, there are duplicate column names. Changing
the hashtagged lines above to use motif_ID instead of motif_name
allows me to run the code without error.

colnames(tf_match) <- motif_df$motif_ID ###
tfs <- motif_df$motif_ID ###

However, since this is mouse, there is still a problem... gene_name and motif_name are mostly human genes. I'm working on the fix for that and will post a separate issue.

As some additional information, I ran WGCNA on the seurat object previously and generated the pfm in this way:

library(JASPAR2024)
library(TFBSTools)
jaspar <- JASPAR2024::JASPAR2024()
sq24 <- RSQLite::dbConnect(RSQLite::SQLite(), db(jaspar))
pfm_core <- getMatrixSet(sq24,
              opts = list(collection = "CORE", 
                          tax_group = 'vertebrates', 
                          all_versions = FALSE))

R session info

r$> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 9.4 (Blue Onyx)

Matrix products: default
BLAS/LAPACK: /datastore/nextgenout5/share/labs/bioinformatics/projects/Serody-Meier-20240314_scRNASeqTcells/scripts/conda/envs/sc-rna-seq/lib/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0

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   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  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] grid      stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] biomaRt_2.58.0                     viridis_0.6.5                      viridisLite_0.4.2                  patchwork_1.2.0                   
 [5] gridExtra_2.3                      GGally_2.2.1                       edgeR_4.0.2                        limma_3.58.1                      
 [9] DESeq2_1.42.0                      ggridges_0.5.6                     pals_1.8                           circlize_0.4.16                   
[13] ComplexHeatmap_2.18.0              SingleCellExperiment_1.24.0        xgboost_2.1.3.1                    BSgenome.Mmusculus.UCSC.mm10_1.4.3
[17] BSgenome_1.70.1                    rtracklayer_1.62.0                 BiocIO_1.12.0                      Biostrings_2.70.1                 
[21] XVector_0.42.0                     EnsDb.Mmusculus.v79_2.99.0         ensembldb_2.26.0                   AnnotationFilter_1.26.0           
[25] GenomicFeatures_1.54.1             AnnotationDbi_1.64.1               TFBSTools_1.40.0                   motifmatchr_1.24.0                
[29] JASPAR2024_0.99.6                  cowplot_1.1.3                      hdWGCNA_0.4.00                     GeneOverlap_1.38.0                
[33] UCell_2.6.2                        tidygraph_1.3.1                    ggraph_2.2.1                       igraph_2.1.2                      
[37] WGCNA_1.73                         fastcluster_1.2.6                  dynamicTreeCut_1.63-1              ggrepel_0.9.5                     
[41] ggalluvial_0.12.5                  harmony_1.2.0                      Rcpp_1.0.12                        Seurat_5.0.3                      
[45] SeuratObject_5.0.1                 sp_2.1-3                           SingleR_2.4.0                      SummarizedExperiment_1.32.0       
[49] Biobase_2.62.0                     GenomicRanges_1.54.1               GenomeInfoDb_1.38.1                IRanges_2.36.0                    
[53] S4Vectors_0.40.2                   MatrixGenerics_1.14.0              matrixStats_1.2.0                  dplyr_1.1.4                       
[57] AnnotationHub_3.10.0               BiocFileCache_2.10.1               dbplyr_2.4.0                       BiocGenerics_0.48.1               
[61] ProjecTILs_3.3.1                   data.table_1.15.2                  ggplot2_3.5.0                      rmarkdown_2.26                    
[65] kableExtra_1.4.0                   knitr_1.45                         docopt_0.7.1                       pander_0.6.5                      

loaded via a namespace (and not attached):
  [1] dichromat_2.0-0.1             R.methodsS3_1.8.2             progress_1.2.3                nnet_7.3-19                   poweRlaw_0.70.6              
  [6] goftest_1.2-3                 vctrs_0.6.5                   spatstat.random_3.2-3         shape_1.4.6.1                 digest_0.6.35                
 [11] png_0.1-8                     proxy_0.4-27                  deldir_2.0-4                  parallelly_1.37.1             MASS_7.3-60                  
 [16] reshape2_1.4.4                httpuv_1.6.15                 foreach_1.5.2                 withr_3.0.0                   xfun_0.43                    
 [21] survival_3.5-8                memoise_2.0.1                 systemfonts_1.1.0             GlobalOptions_0.1.2           zoo_1.8-12                   
 [26] gtools_3.9.5                  pbapply_1.7-2                 R.oo_1.26.0                   prettyunits_1.2.0             Formula_1.2-5                
 [31] KEGGREST_1.42.0               promises_1.2.1                httr_1.4.7                    restfulr_0.0.15               globals_0.16.3               
 [36] fitdistrplus_1.1-11           rstudioapi_0.16.0             miniUI_0.1.1.1                generics_0.1.3                base64enc_0.1-3              
 [41] curl_5.1.0                    zlibbioc_1.48.0               ScaledMatrix_1.10.0           polyclip_1.10-6               GenomeInfoDbData_1.2.11      
 [46] SparseArray_1.2.2             interactiveDisplayBase_1.40.0 xtable_1.8-4                  stringr_1.5.1                 pracma_2.4.4                 
 [51] doParallel_1.0.17             evaluate_0.23                 S4Arrays_1.2.0                preprocessCore_1.64.0         hms_1.1.3                    
 [56] irlba_2.3.5.1                 colorspace_2.1-0              filelock_1.0.3                ROCR_1.0-11                   reticulate_1.35.0            
 [61] spatstat.data_3.0-4           magrittr_2.0.3                lmtest_0.9-40                 readr_2.1.5                   later_1.3.2                  
 [66] lattice_0.22-6                mapproj_1.2.11                spatstat.geom_3.2-9           future.apply_1.11.2           scattermore_1.2              
 [71] XML_3.99-0.16                 RcppAnnoy_0.0.22              Hmisc_5.1-1                   pillar_1.9.0                  nlme_3.1-164                 
 [76] iterators_1.0.14              caTools_1.18.2                compiler_4.3.3                beachmat_2.18.0               RSpectra_0.16-1              
 [81] stringi_1.8.3                 tensor_1.5                    GenomicAlignments_1.38.0      plyr_1.8.9                    crayon_1.5.2                 
 [86] abind_1.4-5                   locfit_1.5-9.9                graphlayouts_1.2.1            bit_4.0.5                     scGate_1.6.0                 
 [91] codetools_0.2-20              BiocSingular_1.18.0           GetoptLong_1.0.5              plotly_4.10.4                 mime_0.12                    
 [96] splines_4.3.3                 fastDummies_1.7.3             sparseMatrixStats_1.14.0      blob_1.2.4                    utf8_1.2.4                   
[101] clue_0.3-65                   BiocVersion_3.18.1            seqLogo_1.68.0                fs_1.6.3                      listenv_0.9.1                
[106] checkmate_2.3.0               DelayedMatrixStats_1.24.0     tibble_3.2.1                  Matrix_1.6-5                  statmod_1.5.0                
[111] tzdb_0.4.0                    svglite_2.1.3                 tweenr_2.0.3                  pkgconfig_2.0.3               pheatmap_1.0.12              
[116] tools_4.3.3                   cachem_1.0.8                  RSQLite_2.3.4                 DBI_1.2.2                     impute_1.76.0                
[121] fastmap_1.1.1                 scales_1.3.0                  ica_1.0-3                     Rsamtools_2.18.0              ggstats_0.5.1                
[126] BiocManager_1.30.22           dotCall64_1.1-1               RANN_2.6.1                    rpart_4.1.23                  farver_2.1.1                 
[131] yaml_2.3.8                    foreign_0.8-86                cli_3.6.2                     purrr_1.0.2                   tester_0.2.0                 
[136] leiden_0.4.3.1                lifecycle_1.0.4               uwot_0.1.16                   backports_1.4.1               BiocParallel_1.36.0          
[141] annotate_1.80.0               gtable_0.3.4                  rjson_0.2.21                  progressr_0.14.0              parallel_4.3.3               
[146] jsonlite_1.8.8                RcppHNSW_0.6.0                bitops_1.0-7                  bit64_4.0.5                   Rtsne_0.17                   
[151] spatstat.utils_3.1-1          BiocNeighbors_1.20.0          CNEr_1.38.0                   R.utils_2.12.3                lazyeval_0.2.2               
[156] shiny_1.8.1                   htmltools_0.5.8               GO.db_3.18.0                  sctransform_0.4.1             rappdirs_0.3.3               
[161] glue_1.7.0                    TFMPvalue_0.0.9               spam_2.10-0                   RCurl_1.98-1.14               R6_2.5.1                     
[166] tidyr_1.3.1                   gplots_3.1.3.1                STACAS_2.2.2                  cluster_2.1.6                 DirichletMultinomial_1.44.0  
[171] ProtGenerics_1.34.0           DelayedArray_0.28.0           tidyselect_1.2.0              maps_3.4.2                    htmlTable_2.4.1              
[176] ggforce_0.4.2                 xml2_1.3.6                    future_1.33.2                 rsvd_1.0.5                    munsell_0.5.1                
[181] KernSmooth_2.23-22            htmlwidgets_1.6.4             RColorBrewer_1.1-3            rlang_1.1.3                   spatstat.sparse_3.0-3        
[186] spatstat.explore_3.2-6        fansi_1.0.6                  

Thanks!
Jen