methyl_circle_plot: Draw methylation circle plot

In markrobinsonuzh/DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions

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)

markrobinsonuzh/DAMEfinder documentation built on April 7, 2023, 6:37 a.m.