decemedip               Main function to perform cell type
                        deconvolution with MeDIP-seq data
decemedip-package       The 'decemedip' package.
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()'
