| methyl_circle_plot {DAMEfinder} | R Documentation |
Draws CpG site methylation status as points, in reads containing a specific SNP. Generates one plot per bam file.
methyl_circle_plot( snp, vcfFile, bamFile, refFile, build = "hg19", dame = NULL, letterSize = 2.5, pointSize = 3, sampleName = "sample1", cpgsite = NULL, sampleReads = FALSE, numReads = 20 )
snp |
GRanges object containing SNP location. |
vcfFile |
vcf file. |
bamFile |
bismark bam file path. |
refFile |
fasta reference file path. Or |
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 |
Plot
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)