dame_track_mean: Plot means per group of score tracks.

In markrobinsonuzh/DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions

Plot means per group of score tracks.

Description

Plot means per group of score tracks.

Usage

dame_track_mean(
  dame,
  window = 0,
  positions = 0,
  derASM = NULL,
  ASM = NULL,
  colvec = NULL
)

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)

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_mean(dame = DAME, 
                ASM = ASM)

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