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 = "cutntag_benchmarking",
  path = getwd(),
  save_dir = file.path(path, "trackhub"),
  folders = c(""),
  domain = "https://webserver-schilder-ukdri.dsi.ic.ac.uk/cutntag_benchmarking",
  shortLabel = "CUT&Tag benchmarking",
  longLabel =
    "Data track associated with the CUT&Tag benchmarking manuscript: https://doi.org/10.1101/2022.03.30.486382",
  email = "",
  visibility = 2,
  genome = "hg19",
  descriptionUrl = paste(save_dir, "description.html", sep = "/"),
  filetypes = c(bigWig = ".bigwig$|.bw$"),
  as_list = TRUE,
  sep = "\t",
  verbose = TRUE
)

Arguments

path	Path to search for files within recursively.
domain	URL prefix where the files will be hosted.
genome	Genome build that files were aligned to.
filetypes	File types to search for.
as_list	Return each file as a nested list.
folder	Subfolders within path to search,
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"))

## End(Not run)

neurogenomics/PeakyFinders documentation built on March 24, 2024, 4:28 p.m.