getJbrowseLink: Generate a url to TREW genome browser

Description Usage Arguments Value Examples

View source: R/trewjb.R

Description

Generate a link to view desired range on the TREW browser according to the suppied arguments.

Usage

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getJbrowseLink(genome, chromosome, range_start, range_end, hight_start,
  hight_end, tracks = c("DNA", "gene_model"),
  baseurl = "http://180.208.58.19/jbrowse", show_navagation = TRUE,
  show_tracklist = FALSE, show_overview = FALSE)

Arguments

genome

Which genome to view, current supported values are "hg19", "mm10" and "dm6".

chromosome

Which chromosome, e.g. "chr1"

range_start, range_end

Length-one numeric vectors to indicate the start and end of the desired range.

hight_start, hight_end

Length-one numeric vectors to indicate the start and end of the hightlight range, if missing, highlight will be disabled.

tracks

Character vectors to indicate which tracks to show. In TREW database, they are also valid experiment id, other primary tracks include "DNA", "gene_model", "all_m6A", "all_m5C", "all_m1A" and "all_Psi". List of available tracks can be found at http://180.208.58.19/jbrowse/ .

baseurl

Default "http://180.208.58.19/jbrowse".

show_navagation

Logical, whether show the navagation parts of the Jbrowse UI?

show_tracklist

Logical, whether show the tracklist parts of the Jbrowse UI?

show_overview

Logical, whether show the overview parts of the Jbrowse UI?

Value

A character as url.

Examples

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if (interactive()) {
    url <- getJbrowseLink("hg19", "chr8", 92114847, 92231464,
        hight_start = 92150113, hight_end = 92152064,
        tracks = c("DNA", "gene_model", "all_m6A"),
        show_tracklist = TRUE, show_overview = TRUE)
    browseURL(url)
}

Marlin-Na/trewjb documentation built on May 7, 2019, 3:36 p.m.