create_trackhub: Create TrackHub

In neurogenomics/PeakyFinders: Mining, Calling, and Importing Epigenomic Peaks in R

Create TrackHub

Description

Create TrackHub for visualization of genomic files in the UCSC Genome Browser.

Usage

create_trackhub(
  hub = "my_hub_name",
  genome,
  path = getwd(),
  save_dir = file.path(path, "trackhub"),
  folders = c(""),
  domain = paste0("https://neurogenomics-ukdri.dsi.ic.ac.uk/", hub),
  shortLabel = "",
  longLabel = "",
  email = "",
  descriptionUrl = paste(save_dir, "description.html", sep = "/"),
  filetypes = c(bed = ".bed$", bigWig = ".bigwig$|.bw$"),
  settings = list(visibility = 2, fontSize = "10", height = "100", autoScale = "on",
    color = "255,102,102", renderer = "BAR_CHART", smoothingWindow = "off",
    windowFunction = "mean", logo = "on"),
  as_list = TRUE,
  sep = "\t",
  verbose = TRUE
)

Arguments

genome	Genome build that files were aligned to.
path	Path to search for files within recursively.
folders	Subfolders within path to search,
domain	URL prefix where the files will be hosted.
filetypes	File types to search for.
settings	Trackhub settings. See UCSC trackhub documentation for details.
as_list	Return each file as a nested list.
save_path	Path to to save trackDb file to.

Value

Character or nested list.

Source

https://genome-euro.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html

https://github.com/mhalushka/UCSC_miRNA_barchart

rtracklayer possible memory leakage

Examples

## Not run: 
path <-"/Volumes/bms20/projects/neurogenomics-lab/live/Projects/CUT_n_TAG/CUTnTag_analysis"
res <- create_trackhub(path=path, folders = c("bigwig","bedgraph","peaks"))

path <-"/Volumes/bms20/projects/neurogenomics-lab/live/Data/tip_seq/processed_data/without_duplicates/tipseq_9_17_jun_2022/"
res <- create_trackhub(hub="tipseq_9_17_jun_2022",
                       path=path, 
                       folders = "03_peak_calling",
                       genome="hg38")

## End(Not run)

neurogenomics/PeakyFinders documentation built on Oct. 14, 2024, 3:09 p.m.