calcTracks: calcTracks

In fmi-basel/gbuehler-MiniChip: MiniChip

calcTracks

Description

Prepare ChIP, repeat, and gene annotation data for plotting tracks for a given region of interest (ROI).

Usage

calcTracks(
  bigwigFiles,
  bigwigNames,
  bigwigGroupNames,
  ROI,
  CoverageSmoothing = TRUE,
  smoothing_window = 20,
  reps,
  genes,
  exons
)

Arguments

bigwigFiles	Character vector containing the filenames (including the full path) of read alignment files in bigwig format.
bigwigNames	Character vector containing the names to describe the bigwigFiles you are using (for example: "H3K9me3_replicate1").
bigwigGroupNames	Character vector containing the group names to describe the bigwigFiles you are using (for example: "H3K9me3").
ROI	A GRanges object containing your single region of interest that should be plotted. Must include seqnames (chromosomes), start, end.
CoverageSmoothing	Logical scalar, indicating whether the coverage tracks should be smoothed. Default: TRUE.
smoothing_window	Numeric scalar providing the window size for smoothing. Default: 20.
reps	A GRanges object containing all repeats in the genome, or at least the ones overlapping the ROI.
genes	A GRanges object containing all genes in the genome, or at least the ones overlapping the ROI.
exons	A GRanges object containing all exons in the genome, or at least the ones overlapping the ROI.

Details

calcTracks is used to prepare ChIP, repeat, and gene annotation data for plotting tracks for a given region of interest (ROI).

Value

A list of data frames containing all necessary information to plot the screenshots using the plotTracks function.

Examples

#see vignette

fmi-basel/gbuehler-MiniChip documentation built on June 13, 2025, 6:15 a.m.