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
Methylation = qs::qread(system.file("extdata", "Methylation_4.qs", package="SingleMoleculeFootprinting"))
RegionOfInterest = GRanges("chr6", IRanges(88106000, 88106500))
TFBSs = qs::qread(system.file("extdata", "TFBSs_1.qs", package="SingleMoleculeFootprinting"))
PlotAvgSMF(MethGR = Methylation[[1]], RegionOfInterest = RegionOfInterest, TFBSs = TFBSs)
## No sorted reads passed...plotting counts from all reads
sessionInfo
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
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## Matrix products: default
## BLAS: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
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## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB 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
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## time zone: America/New_York
## tzcode source: system (glibc)
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## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
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## other attached packages:
## [1] BSgenome.Mmusculus.UCSC.mm10_1.4.3 BSgenome_1.73.1
## [3] rtracklayer_1.65.0 BiocIO_1.15.2
## [5] Biostrings_2.73.2 XVector_0.45.0
## [7] GenomicRanges_1.57.2 GenomeInfoDb_1.41.2
## [9] IRanges_2.39.2 S4Vectors_0.43.2
## [11] BiocGenerics_0.51.3 SingleMoleculeFootprinting_1.99.0
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## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 jsonlite_1.8.9
## [3] magrittr_2.0.3 GenomicFeatures_1.57.1
## [5] farver_2.1.2 rmarkdown_2.28
## [7] zlibbioc_1.51.2 vctrs_0.6.5
## [9] memoise_2.0.1 Rsamtools_2.21.2
## [11] RCurl_1.98-1.16 QuasR_1.45.2
## [13] ggpointdensity_0.1.0 htmltools_0.5.8.1
## [15] S4Arrays_1.5.11 progress_1.2.3
## [17] curl_5.2.3 SparseArray_1.5.45
## [19] sass_0.4.9 bslib_0.8.0
## [21] plyr_1.8.9 httr2_1.0.5
## [23] cachem_1.1.0 GenomicAlignments_1.41.0
## [25] lifecycle_1.0.4 pkgconfig_2.0.3
## [27] Matrix_1.7-1 R6_2.5.1
## [29] fastmap_1.2.0 GenomeInfoDbData_1.2.13
## [31] MatrixGenerics_1.17.0 digest_0.6.37
## [33] colorspace_2.1-1 ShortRead_1.63.2
## [35] patchwork_1.3.0 AnnotationDbi_1.67.0
## [37] RSQLite_2.3.7 hwriter_1.3.2.1
## [39] labeling_0.4.3 filelock_1.0.3
## [41] fansi_1.0.6 httr_1.4.7
## [43] abind_1.4-8 compiler_4.4.1
## [45] Rbowtie_1.45.0 withr_3.0.1
## [47] bit64_4.5.2 BiocParallel_1.39.0
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## [57] tools_4.4.1 glue_1.8.0
## [59] restfulr_0.0.15 grid_4.4.1
## [61] generics_0.1.3 gtable_0.3.5
## [63] tidyr_1.3.1 RApiSerialize_0.1.4
## [65] hms_1.1.3 xml2_1.3.6
## [67] stringfish_0.16.0 utf8_1.2.4
## [69] ggrepel_0.9.6 pillar_1.9.0
## [71] stringr_1.5.1 dplyr_1.1.4
## [73] BiocFileCache_2.13.2 lattice_0.22-6
## [75] bit_4.5.0 deldir_2.0-4
## [77] tidyselect_1.2.1 knitr_1.48
## [79] gridExtra_2.3 SummarizedExperiment_1.35.4
## [81] xfun_0.48 Biobase_2.65.1
## [83] matrixStats_1.4.1 stringi_1.8.4
## [85] UCSC.utils_1.1.0 yaml_2.3.10
## [87] evaluate_1.0.1 codetools_0.2-20
## [89] interp_1.1-6 GenomicFiles_1.41.0
## [91] tibble_3.2.1 cli_3.6.3
## [93] RcppParallel_5.1.9 munsell_0.5.1
## [95] jquerylib_0.1.4 Rcpp_1.0.13
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## [105] latticeExtra_0.6-30 jpeg_0.1-10
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