FootprintCharter

Introduction

This vignette exemplifies how to perform unsupervised footprint detection and quantification using FootprintCharter as per Baderna & Barzaghi et al., 2024 and Barzaghi et al., 2024.

FootprintCharter partitions molecules by their methylation patterns without relying on orthogonal genomic annotations such as TF motifs.

Loading libraries

suppressWarnings(library(SingleMoleculeFootprinting))
suppressWarnings(library(BSgenome.Mmusculus.UCSC.mm10))

sessionInfo

## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [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       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] BSgenome.Mmusculus.UCSC.mm10_1.4.3 BSgenome_1.75.0                   
##  [3] rtracklayer_1.66.0                 BiocIO_1.17.0                     
##  [5] Biostrings_2.75.0                  XVector_0.46.0                    
##  [7] GenomicRanges_1.59.0               GenomeInfoDb_1.43.0               
##  [9] IRanges_2.41.0                     S4Vectors_0.44.0                  
## [11] BiocGenerics_0.53.1                generics_0.1.3                    
## [13] SingleMoleculeFootprinting_2.1.0  
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3          sys_3.4.3                  
##   [3] jsonlite_1.8.9              magrittr_2.0.3             
##   [5] GenomicFeatures_1.59.0      farver_2.1.2               
##   [7] rmarkdown_2.28              zlibbioc_1.52.0            
##   [9] vctrs_0.6.5                 memoise_2.0.1              
##  [11] Rsamtools_2.22.0            RCurl_1.98-1.16            
##  [13] QuasR_1.46.0                ggpointdensity_0.1.0       
##  [15] htmltools_0.5.8.1           S4Arrays_1.6.0             
##  [17] progress_1.2.3              curl_5.2.3                 
##  [19] SparseArray_1.6.0           sass_0.4.9                 
##  [21] bslib_0.8.0                 plyr_1.8.9                 
##  [23] httr2_1.0.5                 cachem_1.1.0               
##  [25] buildtools_1.0.0            GenomicAlignments_1.43.0   
##  [27] lifecycle_1.0.4             pkgconfig_2.0.3            
##  [29] Matrix_1.7-1                R6_2.5.1                   
##  [31] fastmap_1.2.0               GenomeInfoDbData_1.2.13    
##  [33] MatrixGenerics_1.19.0       digest_0.6.37              
##  [35] colorspace_2.1-1            ShortRead_1.64.0           
##  [37] patchwork_1.3.0             AnnotationDbi_1.69.0       
##  [39] RSQLite_2.3.7               hwriter_1.3.2.1            
##  [41] labeling_0.4.3              filelock_1.0.3             
##  [43] fansi_1.0.6                 httr_1.4.7                 
##  [45] abind_1.4-8                 compiler_4.4.1             
##  [47] Rbowtie_1.46.0              withr_3.0.2                
##  [49] bit64_4.5.2                 BiocParallel_1.41.0        
##  [51] viridis_0.6.5               DBI_1.2.3                  
##  [53] qs_0.27.2                   highr_0.11                 
##  [55] biomaRt_2.63.0              rappdirs_0.3.3             
##  [57] DelayedArray_0.33.1         rjson_0.2.23               
##  [59] tools_4.4.1                 glue_1.8.0                 
##  [61] restfulr_0.0.15             grid_4.4.1                 
##  [63] gtable_0.3.6                tidyr_1.3.1                
##  [65] RApiSerialize_0.1.4         hms_1.1.3                  
##  [67] stringfish_0.16.0           xml2_1.3.6                 
##  [69] utf8_1.2.4                  ggrepel_0.9.6              
##  [71] pillar_1.9.0                stringr_1.5.1              
##  [73] dplyr_1.1.4                 BiocFileCache_2.15.0       
##  [75] lattice_0.22-6              bit_4.5.0                  
##  [77] deldir_2.0-4                tidyselect_1.2.1           
##  [79] maketools_1.3.1             knitr_1.48                 
##  [81] gridExtra_2.3               SummarizedExperiment_1.36.0
##  [83] xfun_0.48                   Biobase_2.67.0             
##  [85] matrixStats_1.4.1           stringi_1.8.4              
##  [87] UCSC.utils_1.2.0            yaml_2.3.10                
##  [89] evaluate_1.0.1              codetools_0.2-20           
##  [91] interp_1.1-6                GenomicFiles_1.43.0        
##  [93] tibble_3.2.1                cli_3.6.3                  
##  [95] RcppParallel_5.1.9          munsell_0.5.1              
##  [97] jquerylib_0.1.4             Rcpp_1.0.13                
##  [99] dbplyr_2.5.0                tidyverse_2.0.0            
## [101] png_0.1-8                   XML_3.99-0.17              
## [103] parallel_4.4.1              ggplot2_3.5.1              
## [105] blob_1.2.4                  prettyunits_1.2.0          
## [107] latticeExtra_0.6-30         jpeg_0.1-10                
## [109] plyranges_1.27.0            bitops_1.0-9               
## [111] pwalign_1.3.0               txdbmaker_1.2.0            
## [113] viridisLite_0.4.2           VariantAnnotation_1.52.0   
## [115] scales_1.3.0                purrr_1.0.2                
## [117] crayon_1.5.3                rlang_1.1.4                
## [119] KEGGREST_1.47.0