plotDMRs: Converts annotated DMRs in a plot

In GianlucaMattei/methyl.O: Annotate, Score and Visualize Differentially Methylated Regions

Converts annotated DMRs in a plot

Description

This function allows to track in a plot the beta value of a methylated segment mapped on a transcript of the human genome

Usage

plotDMRs(
  annotatedDMRs,
  symbol,
  annotation = "ensembl",
  hg = "hg19",
  beta1.name = NULL,
  beta2.name = NULL,
  beta.colors = c("red", "navy"),
  blackandwhite = FALSE,
  show.all.transcripts = FALSE,
  prom.width = 1500,
  path = NULL,
  coord.zoom = NULL,
  smartzoom = TRUE,
  height.pdf = 9,
  width.pdf = 16
)

Arguments

annotatedDMRs	anotated DMRs list resultingfrom annotateDMRs() or scoreAnnotatedDMRs()
symbol	character, gene symbol to plot.
annotation	character, "ensembl" or "ucsc". Annotation used to track the plot. Default = "esembl".
hg	character, "hg19" or "hg38". Genome Assembly version. Default = "hg19".
beta1.name	character, if unsued beta difference is plotted. character string identifying beta value of first sample in "other" column in results from annotateDMRs() or indentifying colname in input table used in annotateDMRs()
beta2.name	character, it identifies beta value of second sample in "other" column in results from annotateDMRs() or it identifies colname in input table used in annotateDMRs()
beta.colors	character vectors, colors of tracks for the first and the second bvalue, respectivetely. Default is c("red", "navy"). If beta diff is plotted, only the first element of vector is considered.
blackandwhite	logical, it allows to get all the plot in greyscale. Default = FALSE.
show.all.transcripts	logical, if TRUE all transcripts of genes are tracked, if FALSE only the longest transcript is tracked. Default = FALSE.
prom.width	integer, promoter lenght. Default = 1500.
path	logical, path where the plot is saved in a pdf file. If NULL the plot is not saved. Default = NULL.
coord.zoom	numeric vectors, coordinates of zoom region. If NULL the plot is not zoomed. Default = NULL.
smartzoom	logical, automatic zoom on the methylated region. Default = TRUE.
height.pdf	integer, hight pdf file. Default = 9.
width.pdf	integer, width pdf file. Default = 16.

Value

Plot of the beta value(s) mapped on transcript(s).

GianlucaMattei/methyl.O documentation built on Sept. 12, 2023, 11:53 p.m.