dame_track: Plot score tracks

In DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions

Description

Plot score tracks

Usage

dame_track(
  dame,
  window = 0,
  positions = 0,
  derASM = NULL,
  ASM = NULL,
  colvec = NULL,
  plotSNP = FALSE
)

Arguments

dame	GRanges object containing a region of interest, or detected with find_dames
window	Number of CpG sites outside (up or down-stream) of the DAME should be plotted. Default = 0.
positions	Number of bp sites outside (up or down-stream) of the DAME should be plotted. Default = 0.
derASM	SummarizedExperiment object obtained from calc_derivedasm (Filtering should be done by the user)
ASM	SummarizedExperiment object obtained from calc_asm (Filtering should be done by the user)
colvec	Vector of colors (mainly useful for the SNP plot, because I add it with cowplot, so I don't export a ggplot, optional)
plotSNP	whether to add the SNP track, only if derASM is specified. Default = FALSE

Value

Plot

Examples

library(GenomicRanges)
DAME <- GRanges(19, IRanges(306443,310272))
data('readtuples_output')
ASM <- calc_asm(readtuples_output)
SummarizedExperiment::colData(ASM)$group <- c(rep('CRC',3),rep('NORM',2))
SummarizedExperiment::colData(ASM)$samples <- colnames(ASM)
dame_track(dame = DAME, 
           ASM = ASM) 

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