Observed and expected profile of one motif in one sample

Usage

plotExpectedAccFootprint(
  motif,
  tf_bindsites,
  ins,
  sample_name = NULL,
  gc_dist,
  gcfreqs,
  enhancer = NULL,
  ignoreStrand = TRUE,
  smooth = 5L,
  returnPlotData = FALSE
)

Arguments

motif: Motif name.
tf_bindsites: A GRangesList of binding site positions.
ins: A GRanges of insertion sites.
sample_name: Optional sample label.
gc_dist: A GRanges of the genome wide GC distribution.
gcfreqs: A list of GC bin frequency tables.
enhancer: Optional GRanges restricting the sites.
ignoreStrand: If TRUE, strand information is ignored.
smooth: Width of the running mean applied to the profiles.
returnPlotData: If TRUE, the plot data is returned as well.

Value

A ggplot object, or a list with the plot and its data.

Examples

if (FALSE) { # \dontrun{
plotExpectedAccFootprint("CTCF", tf_bindsites, ins,
    gc_dist = gc_dist, gcfreqs = gcfreqs)
} # }