methyl_circle_plotCpG: Draw methylation circle plot without SNP

In DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions

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)

DAMEfinder documentation built on Nov. 8, 2020, 11:10 p.m.