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

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Documentation for package ‘decemedip’ version 0.99.8

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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()'