transcriptWindow: Make 100 bases size meta window for all libraries in...
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Value See Also Examples

Gives you binned meta coverage plots, either saved seperatly or all in one.

transcriptWindow(
  leaders,
  cds,
  trailers,
  df,
  outdir = NULL,
  scores = c("sum", "zscore"),
  allTogether = TRUE,
  colors = experiment.colors(df),
  title = "Coverage metaplot",
  windowSize = min(100, min(widthPerGroup(leaders, FALSE)), min(widthPerGroup(cds,
    FALSE)), min(widthPerGroup(trailers, FALSE))),
  returnPlot = is.null(outdir),
  dfr = NULL,
  idName = "",
  format = ".png",
  type = "ofst",
  is.sorted = FALSE,
  BPPARAM = bpparam()
)

`leaders`	a `GRangesList` of leaders (5' UTRs)
`cds`	a `GRangesList` of coding sequences
`trailers`	a `GRangesList` of trailers (3' UTRs)
`df`	an ORFik `experiment`
`outdir`	directory to save to (default: NULL, no saving)
`scores`	scoring function (default: c("sum", "zscore")), see ?coverageScorings for possible scores.
`allTogether`	plot all coverage plots in 1 output? (defualt: TRUE)
`colors`	Which colors to use, default auto color from function `experiment.colors`, new color per library type. Else assign colors yourself.
`title`	title of ggplot
`windowSize`	size of binned windows, default: 100
`returnPlot`	return plot from function, default is.null(outdir), so TRUE if outdir is not defined.
`dfr`	an ORFik `experiment` of RNA-seq to normalize against. Will add RNA normalized to plot name if this is done.
`idName`	A character ID to add to saved name of plot, if you make several plots in the same folder, and same experiment, like splitting transcripts in two groups like targets / nontargets etc. (default: "")
`format`	default (".png"), do ".pdf" if you want as pdf
`type`	a character(default: "bedoc"), load files in experiment or some precomputed variant, either "bedo", "bedoc", "pshifted" or default. These are made with ORFik:::simpleLibs(), shiftFootprintsByExperiment().. Will load default if bedoc is not found
`is.sorted`	logical (FALSE), is grl sorted. That is + strand groups in increasing ranges (1,2,3), and - strand groups in decreasing ranges (3,2,1)
`BPPARAM`	how many cores/threads to use? default: bpparam()

NULL, or ggplot object if returnPlot is TRUE

Other experiment plots: transcriptWindow1(), transcriptWindowPer()

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df <- ORFik.template.experiment()[3,] # Only third library
loadRegions(df) # Load leader, cds and trailers as GRangesList
#transcriptWindow(leaders, cds, trailers, df, outdir = "directory/to/save")