create_hub: Create UCSC track hub for BigWig files

In LieberInstitute/recount3: Explore and download data from the recount3 project

Create UCSC track hub for BigWig files

Description

This function creates a directory with the configuration files required for creating a UCSC track hub for the BigWig files from a given project. These files can then be hosted on GitHub or elsewhere. For more details about UCSC track hubs, check https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html.

Usage

create_hub(
  x,
  output_dir = file.path(tempdir(), x$project[1]),
  hub_name = "recount3",
  email = "someone@somewhere",
  show_max = 5,
  hub_short_label = "recount3 coverage",
  hub_long_label =
    "recount3 summaries and queries for large-scaleRNA-seq expression and splicing",
  hub_description_url = "https://rna.recount.bio/index.html",
  recount3_url = getOption("recount3_url", "http://duffel.rail.bio/recount3")
)

Arguments

x	A data.frame created with available_samples() that has typically been subset to a specific project ID from a given organism.
output_dir	A character(1) with the output directory.
hub_name	A character(1) with the UCSC track hub name you want to display.
email	A character(1) with the email used for the UCSC track hub.
show_max	An integer(1) with the number of BigWig tracks to show by default in the UCSC track hub. We recommend a single digit number.
hub_short_label	A character(1) with the UCSC track hub short label.
hub_long_label	A character(1) with the UCSC track hub long label.
hub_description_url	A character(1) with the URL to an html file that will describe the UCSC track hub to users.
recount3_url	A character(1) specifying the home URL for recount3 or a local directory where you have mirrored recount3. Defaults to the load balancer http://duffel.rail.bio/recount3, but can also be https://recount-opendata.s3.amazonaws.com/recount3/release from https://registry.opendata.aws/recount/ or SciServer datascope from IDIES at JHU https://sciserver.org/public-data/recount3/data. You can set the R option recount3_url (for example in your .Rprofile) if you have a favorite mirror.

Details

See https://github.com/LieberInstitute/recount3-docs/blob/master/UCSC_hubs/create_hubs.R for an example of how this function was used.

Value

A directory at output_dir with the files needed for a UCSC track hub.

Examples

## Find all the mouse samples available from recount3
mouse_samples <- available_samples("mouse")

## Subset to project DRP001299
info_DRP001299 <- subset(mouse_samples, project == "DRP001299")

hub_dir <- create_hub(info_DRP001299)

## List the files created by create_hub()
hub_files <- list.files(hub_dir, full.names = TRUE, recursive = TRUE)
hub_files

## Check the files contents
sapply(hub_files, function(x) {
    cat(paste(readLines(x), collapse = "\n"))
})

## You can also check the file contents for this example project at
## https://github.com/LieberInstitute/recount3-docs/tree/master/UCSC_hubs/mouse/sra_DRP001299
## or test it out on UCSC directly through the following URL:
## https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1&hubUrl=https://raw.githubusercontent.com/LieberInstitute/recount3-docs/master/UCSC_hubs/mouse/sra_DRP001299/hub.txt

LieberInstitute/recount3 documentation built on May 10, 2023, 6:01 a.m.