# hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylome

## Documentation for package ‘decemedip’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

decemedip-package | The 'decemedip' package.
decemedip | Main function to perform cell type deconvolution with MeDIP-seq data
example.hg19.ref.anc.se | Subset of hg19.ref.anc.se as a lightweighted example
example.hg19.ref.cts.se | Subset of hg19.ref.cts.se as a lightweighted example
example.pdx.counts.anc.se | Subset of pdx.counts.anc.se as a lightweighted example
example.pdx.counts.cts.se | Subset of pdx.counts.cts.se as a lightweighted example
getRoiReadCount | Obtain read counts of regions of interest from MeDIP-seq bam files
getSummaryOnPi | Extract summary statistics and diagnostics on fitted cell type proportions
hg19.ref.anc.se | Hg19 genomic information of anchor CpGs (i.e., all-tissue unmethylated/methylation probes) inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6). Used as default in 'decemedip'.
hg19.ref.cts.se | Hg19 genomic information of cell-type-specific marker CpGs inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6).
hg38.ref.anc.se | Hg38 genomic information of cell-type-specific marker CpGs inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6).
hg38.ref.cts.se | Hg38 genomic information of cell-type-specific marker CpGs inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6).
makeReferencePanel | Function for assembling a SummarizedExperiment object of reference panel in *hg19* for cell type deconvolution (which is used in 'decemedip' function)
pdx.counts.anc.se | MeDIP-seq read counts on reference anchor CpGs of 3 PDX samples from Berchuck et al. 2022
pdx.counts.cts.se | MeDIP-seq read counts on reference cell type-specific CpGs of 3 PDX samples from Berchuck et al. 2022
plotDiagnostics | Diagnostics for model fitting in 'decemedip()'