Package {ImprintCapASM}

Run Allele-Specific Methylation Analysis

Description

Performs SNP-phased allele-specific methylation (ASM) analysis across the canonical human imprinted differentially methylated regions (DMRs). Reads are assigned to REF or ALT alleles based on bisulfite-aware SNP detection, and per-allele CpG methylation fractions are computed.

Usage

ASM(
  cpg_snp_file,
  sam_file,
  filter_cpgs_file,
  output_file = NULL,
  sample_type = c("control", "patient"),
  verbose = TRUE
)

Arguments

Value

A named list with three elements:

asm

Full read-level ASM results as a data.table.

snp_cpg

Per SNP x CpG summary table.

meth_summary

Per CpG allele methylation summary table.

Examples

## Not run: 
  extdata     <- system.file("extdata", package = "ImprintCapASM")
  cpg_snp_tmp <- tempfile(fileext = ".xlsx")

  prepare_cpg_snp_input(
    snp_file     = file.path(extdata, "example_snp.out"),
    meth_file    = file.path(extdata, "example_cgmeth.txt"),
    cpg_ref_file = file.path(extdata, "example_filter_cpgs.xlsx"),
    output_file  = cpg_snp_tmp,
    sample_type  = "control"
  )

  result <- ASM(
    cpg_snp_file     = cpg_snp_tmp,
    sam_file         = file.path(extdata, "example_markdup.bam"),
    filter_cpgs_file = file.path(extdata, "example_filter_cpgs.xlsx"),
    output_file      = tempfile(fileext = ".xlsx"),
    sample_type      = "control"
  )
  head(result$snp_cpg)

## End(Not run)

Extract BAM Regions Around SNP Windows

Description

Calls samtools view and samtools sort to subset a whole-genome bisulfite BAM file to the genomic windows defined in a BED file, producing a smaller indexed BAM suitable for input to ASM.

Usage

extract_bam_regions(
  bam_file,
  bed_file,
  output_dir = dirname(bam_file),
  overwrite = FALSE,
  sample_type = c("control", "patient"),
  verbose = TRUE
)

Arguments

Details

Requires samtools to be available on the system PATH. The function calls samtools view -b, samtools sort, and samtools index in sequence. If no .bai index is found alongside bam_file, indexBam is called automatically.

Value

The path to the output BAM file (returned invisibly).

Examples

if (nchar(Sys.which("samtools")) > 0L) {
  extdata <- system.file("extdata", package = "ImprintCapASM")

  out_bam <- extract_bam_regions(
    bam_file    = file.path(extdata, "example_markdup.bam"),
    bed_file    = file.path(extdata, "example_cpg_snp.bed"),
    output_dir  = tempdir(),
    sample_type = "control"
  )
  file.exists(out_bam)
}

Prepare CpG-SNP Input Table

Description

Loads a bisulfite SNP .out file and a CpG methylation file, intersects heterozygous SNPs with the 41-DMR CpG panel, and returns a per-sample CpG-SNP pair table ready for input to ASM.

Usage

prepare_cpg_snp_input(
  snp_file,
  meth_file,
  cpg_ref_file,
  output_file = NULL,
  min_depth = 20L,
  window_bp = 60L,
  sample_type = c("control", "patient"),
  verbose = TRUE
)

Arguments

Value

A data.table of CpG-SNP pairs (returned invisibly). The .xlsx and .bed files are written as side effects.

Examples

  extdata    <- system.file("extdata", package = "ImprintCapASM")
  cpg_snp_tmp <- tempfile(fileext = ".xlsx")

  result <- prepare_cpg_snp_input(
    snp_file     = file.path(extdata, "example_snp.out"),
    meth_file    = file.path(extdata, "example_cgmeth.txt"),
    cpg_ref_file = file.path(extdata, "example_filter_cpgs.xlsx"),
    output_file  = cpg_snp_tmp,
    sample_type  = "control"
  )
  head(result)

Run the Full ImprintCapASM Pipeline

Description

Convenience wrapper that executes the complete three-step pipeline: (1) prepare_cpg_snp_input, (2) extract_bam_regions, and (3) ASM for every sample in a directory. Controls and patients are always processed independently using their respective filter_cpgs reference files.

Usage

run_pipeline(
  bam_dir,
  snp_dir,
  meth_dir,
  cpg_ref_file,
  output_dir,
  sample_type = c("control", "patient"),
  bed_file,
  min_depth = 20L,
  window_bp = 60L,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

Value

Invisibly returns a named list of ASM result objects, one per sample. Each element is the list returned by ASM, containing $asm, $snp_cpg, and $meth_summary.

Examples

## Not run: 
  extdata    <- system.file("extdata", package = "ImprintCapASM")
  cpg_ref    <- file.path(extdata, "example_filter_cpgs.xlsx")
  bed        <- file.path(extdata, "example_cpg_snp.bed")
  output_dir <- tempdir()

  results <- run_pipeline(
    bam_dir      = extdata,
    snp_dir      = extdata,
    meth_dir     = extdata,
    cpg_ref_file = cpg_ref,
    output_dir   = output_dir,
    sample_type  = "control",
    bed_file     = bed
  )
  head(results[[1]]$asm)

## End(Not run)