methyl_circle_plot {DAMEfinder} | R Documentation

## Draw methylation circle plot

### Description

Draws CpG site methylation status as points, in reads containing a specific SNP. Generates one plot per bam file.

### Usage

    methyl_circle_plot(
      snp,
      vcfFile,
      bamFile,
      refFile,
      build = "hg19",
      dame = NULL,
      letterSize = 2.5,
      pointSize = 3,
      sampleName = "sample1",
      cpgsite = NULL,
      sampleReads = FALSE,
      numReads = 20
    )

### Arguments

`snp` | GRanges object containing SNP location.
`vcfFile` | vcf file.
`bamFile` | bismark bam file path.
`refFile` | fasta reference file path. Or `DNAStringSet` with DNA sequence.
`build` | genome build used. default = "hg19"
`dame` | (optional) GRanges object containing a region to plot.
`letterSize` | Size of alleles drawn in plot. Default = 2.5.
`pointSize` | Size of methylation circles. Default = 3.
`sampleName` | FIX?: this is to save the vcf file to not generate it every time you run the function.
`cpgsite` | (optional) GRanges object containing a single CpG site location of interest.
`sampleReads` | Whether a subset of reads should be plotted. Default = FALSE.
`numReads` | Number of reads to plot per allele, if sampleReads is TRUE. Default = 20

### Value

Plot

### Examples

    DATA_PATH_DIR <- system.file('extdata', '.', package = 'DAMEfinder')

    get_data_path <- function(file_name) file.path(DATA_PATH_DIR, file_name)
    bam_files <- get_data_path('NORM1_chr19_trim.bam')
    vcf_files <- get_data_path('NORM1.chr19.trim.vcf')
    sample_names <- 'NORM1'
    #reference_file
    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

    snp <- GenomicRanges::GRanges(19, IRanges::IRanges(292082, width = 1))
    methyl_circle_plot(snp = snp,
     vcfFile = vcf_files,
     bamFile = bam_files,
     refFile = dna,
     sampleName = sample_names)

[Package DAMEfinder version 1.6.0 Index]