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: /home/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:
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## [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
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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_1.74.0
## [3] rtracklayer_1.66.0 BiocIO_1.16.0
## [5] Biostrings_2.74.0 XVector_0.46.0
## [7] GenomicRanges_1.58.0 GenomeInfoDb_1.42.0
## [9] IRanges_2.40.0 S4Vectors_0.44.0
## [11] BiocGenerics_0.52.0 SingleMoleculeFootprinting_2.0.0
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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_1.58.0
## [5] farver_2.1.2 rmarkdown_2.28
## [7] zlibbioc_1.52.0 vctrs_0.6.5
## [9] memoise_2.0.1 Rsamtools_2.22.0
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## [13] ggpointdensity_0.1.0 htmltools_0.5.8.1
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## [29] fastmap_1.2.0 GenomeInfoDbData_1.2.13
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