methyl_circle_plotCpG {DAMEfinder} | R Documentation |
Draws CpG site methylation status as points, in reads containing a specific CpG site. Generates one plot per bam file.
methyl_circle_plotCpG( cpgsite = cpgsite, bamFile = bamFile, pointSize = 3, refFile = refFile, dame = NULL, order = FALSE, sampleName = NULL, sampleReads = FALSE, numReads = 20 )
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 |
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') 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)