## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

## ----setup--------------------------------------------------------------------
# library(ImprintCapASM)

## ----install------------------------------------------------------------------
# install.packages("ImprintCapASM")

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

## ----step1--------------------------------------------------------------------
# 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"
# )

## ----step2--------------------------------------------------------------------
# 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"
# )

## ----step3--------------------------------------------------------------------
# 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"
# )