dame_track: Plot score tracks

View source: R/score_tracks.R

dame_trackR Documentation

Plot score tracks

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) 


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