Last updated: 2026-01-21

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Knit directory: fsusie-experiments/analysis/

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Load the example DNA methylation (WGBS) and H3K9ac (ChIP-seq) signals.

load("../data/smash_meth_ha.RData")

Load smashr:

library(smashr)

Set the seed to make the results reproducible:

set.seed(1)

WGBS DNA methylation example

This plot shows the beta values at the CpG locations for a single sample (black dots) and the “smoothed” signal obtained by running SMASH on these data (blue curve):

y <- methyl_dat$beta
res <- smash.gaus(y,v.est = FALSE)
plot(y,pch = 20,col = "black",cex = 0.65,xlab = "CpG",ylab = "beta value")
lines(res,type = "l",col = "royalblue")

Version Author Date
2563850 Peter Carbonetto 2026-01-21

Note that the CpG locations are ordered sequencing by base-pair position along the chromosome (specifically, chromosome 20, near gene CASS4). However, the positions of the CpG probes are not distributed uniformly; there are some large gaps where there is no probe. The methylation data are shown in this way to make the spatial structure more obvious.

ChIP-seq H3K9ac example

This plot shows the read count data from the ChIP-seq assay (black dots) and the “smoothed” signal obtained by running SMASH on these data (blue curve):

y <- h3k9ac_dat$y
pos <- h3k9ac_dat$pos
res <- smash.poiss(y,post.var = FALSE)
plot(pos/1e6,y,pch = 20,col = "black",
     xlab = "base-pair position on chromosome 1 (Mb)",
     ylab = "read count")
lines(pos/1e6,res,type = "l",col = "royalblue")

Version Author Date
2563850 Peter Carbonetto 2026-01-21

This the H3K9ac signal from a region on chromosome 1 near genes CR1 and CR2.

Note that since these are counts, we used the Poisson-based SMASH method. Also note that the read counts are actually read counts averaged across a few samples, so the read counts are not actually integers.


sessionInfo()
# R version 4.3.3 (2024-02-29)
# Platform: aarch64-apple-darwin20 (64-bit)
# Running under: macOS 15.7.1
# 
# Matrix products: default
# BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
# LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
# 
# locale:
# [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
# 
# time zone: America/Chicago
# tzcode source: internal
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] smashr_1.3-12
# 
# loaded via a namespace (and not attached):
#  [1] Matrix_1.6-5      jsonlite_2.0.0    compiler_4.3.3    promises_1.3.3   
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