# ImprintCapASM-workflow

    library(ImprintCapASM)

## Overview

ImprintCapASM is a three-step pipeline for SNP-phased allele-specific methylation (ASM) analysis across the 41 known imprinted differentially methylated regions (DMRs). It accepts a VCF SNP file, a bisulfite methylation table, and an aligned BAM file, and returns per-allele methylation fractions, summary tables, and diagnostic plots per DMR.

## Installation

    install.packages("ImprintCapASM")

## Requirements

- R >= 4.1.0
- `samtools` must be installed and on your system PATH
- R packages: `data.table`, `vcfR`, `readxl`, `writexl`, `ggplot2`, `Rsamtools`

## Input files

Place the following files in your `input/` folder:

File | Description
--- | ---
`SAMPLEID_all.SNPs.out` | VCF SNP calls from bisulfite sequencing
`SAMPLEID_all.CGmeth.txt` | Bisulfite methylation table
`SAMPLEID_all_markdup.bam` | Aligned, duplicate-marked BAM file

The reference file `data/filter_Cpgs.xlsx` is bundled with the package.

## Running the full pipeline

    source("run_pipeline.R")
    # You will be prompted:
    # Enter sample type [control / patient]: control

## Step 1 — prepare_cpg_snp_input()

    prepare_cpg_snp_input(
      snp_file     = "input/SAMPLE_all.SNPs.out",
      meth_file    = "input/SAMPLE_all.CGmeth.txt",
      cpg_ref_file = "data/filter_Cpgs.xlsx",
      output_file  = "asm_results/cpg_snps_control_SAMPLE.xlsx",
      sample_type  = "control"
    )

## Step 2 — extract_bam_regions()

    extract_bam_regions(
      bam_file    = "input/SAMPLE_all_markdup.bam",
      bed_file    = "asm_results/cpg_snps_control_SAMPLE.bed",
      output_dir  = "bam_asm/",
      sample_type = "control"
    )

## Step 3 — ASM()

    ASM(
      cpg_snp_file     = "asm_results/cpg_snps_control_SAMPLE.xlsx",
      sam_file         = "bam_asm/control_SAMPLE_all_wide.bam",
      filter_cpgs_file = "data/filter_Cpgs.xlsx",
      output_file      = "asm_results/asm_control_SAMPLE.xlsx",
      sample_type      = "control"
    )

## Output files

File | Contents
--- | ---
`asm_<type>_<id>.xlsx` | Full read-level ASM table
`snp_cpg_<type>_<id>.xlsx` | Per SNP×CpG methylation fractions
`meth_summary_<type>_<id>.xlsx` | Allele methylation summary per DMR
`dmr_plots_<type>_<id>.pdf` | Diagnostic line plots per DMR