dame_track {DAMEfinder} | R Documentation |
Plot score tracks
dame_track( dame, window = 0, positions = 0, derASM = NULL, ASM = NULL, colvec = NULL, plotSNP = FALSE )
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 |
Plot
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)