Last updated: 2020-09-21

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Rmd bd4a4c8 DongyueXie 2020-09-21 wflow_publish(c(“analysis/contrainedclustering.Rmd”, “analysis/count.Rmd”,

DNA Mehylation vs enhancer/promoter?

What is nucleosome positions. Combine single cell? how? why? sliding window?

Another way to use single cell data would be to get a measurement for each cell (with coverage) at regions that were identified as peaks or nucleosomes and that way get a measurement of heterogeneity.??

BPRMeth

Inputs are Binomial DNA methylation data, with postions \(x\). Tasks are 1. smooth each binomial sequences; 2. perform clustering on multiple DNA methylation sequences.(how? each seq is of different length) 3. binomial data can be bernoulli in single cell case.

BSmooth

Introduction

Try BPRMeth package.


R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
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 [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       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
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[13] promises_1.0.1  whisker_0.3-2   rmarkdown_1.10  tools_3.5.1    
[17] stringr_1.3.1   glue_1.3.0      httpuv_1.4.5    yaml_2.2.0     
[21] compiler_3.5.1  htmltools_0.3.6 knitr_1.20