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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

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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