Package index • decemedip

All functions

decemedip-package: The 'decemedip' package.

decemedip(): Main function to perform cell type deconvolution with MeDIP-seq data

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.cpg.coords: Genomic information of CpG positions in hg19

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