extract_bams {DAMEfinder} | R Documentation

## Detect allele-specific methylation from a bam file

### Description

The function takes a bam (from bismark) and vcf file for each sample. For each SNP contained in the vcfile it calculates the proportion of methylated reads for each CpG site at each allele. At the end it returns (saves to working directory) a GRanges list, where each GRanges contains all the CpG sites overlapping the reads containing a specific SNP.

### Usage

    extract_bams(
      bamFiles,
      vcfFiles,
      sampleNames,
      referenceFile,
      coverage = 4,
      cores = 1,
      verbose = TRUE
    )

### Arguments

`bamFiles` | List of bam files.
`vcfFiles` | List of vcf files.
`sampleNames` | Names of files in the list.
`referenceFile` | fasta file used to generate the bam files. Or `DNAStringSet` with DNA sequence.
`coverage` | Minimum number of reads covering a CpG site on each allele. Default = 2.
`cores` | Number of cores to use. See package parallel for description of core. Default = 1.
`verbose` | Default = TRUE

### Value

A list of GRanges for each sample. Each list is saved in a separate .rds file.

### Examples

    DATA_PATH_DIR <- system.file('extdata', '.', package = 'DAMEfinder')
    get_data_path <- function(file_name) file.path(DATA_PATH_DIR, file_name)
    bamFiles <- get_data_path('NORM1_chr19_trim.bam')
    vcfFiles <- get_data_path('NORM1.chr19.trim.vcf')
    sampleNames <- 'NORM1'

    #referenceFile
    suppressPackageStartupMessages({library(BSgenome.Hsapiens.UCSC.hg19)})
    genome <- BSgenome.Hsapiens.UCSC.hg19
    seqnames(genome) <- gsub("chr","",seqnames(genome))
    dna <- DNAStringSet(genome[[19]], use.names = TRUE)
    names(dna) <- 19

    GRanges_list <- extract_bams(bamFiles, vcfFiles, sampleNames, dna)

[Package DAMEfinder version 1.2.0 Index]