methyl_circle_plotCpG {DAMEfinder} | R Documentation

## Draw methylation circle plot without SNP

### Description

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

### Usage

    methyl_circle_plotCpG(
      cpgsite = cpgsite,
      bamFile = bamFile,
      pointSize = 3,
      refFile = refFile,
      dame = NULL,
      order = FALSE,
      sampleName = NULL,
      sampleReads = FALSE,
      numReads = 20
    )

### Arguments

`cpgsite` | GRanges object containing a single CpG site location of interest
`bamFile` | bismark bam file path
`pointSize` | Size of methylation circles. Default = 3.
`refFile` | fasta reference file path
`dame` | (optional) GRanges object containing a region to plot
`order` | Whether reads should be sorted by methylation status. Default= False.
`sampleName` | Plot title.
`sampleReads` | Whether a subset of reads should be plotted. Default = FALSE.
`numReads` | Number of reads to plot, 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')
    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

    cpg <- GenomicRanges::GRanges(19, IRanges::IRanges(292082, width = 1))
    methyl_circle_plotCpG(cpgsite = cpg,
     bamFile = bam_files,
     refFile = dna)

[Package DAMEfinder version 1.6.0 Index]