make_rc_url: Create URL to browse a gene on Ribocrypt webpage

In Miswi/RiboCrypt: Interactive visualization in genomics

Create URL to browse a gene on Ribocrypt webpage

Description

Can also make url for local RiboCrypt app' On the actuall app, the function make_url_from_inputs is used on the shiny reactive input object. This one is for manual use.

Usage

make_rc_url(
  symbol = NULL,
  gene_id = NULL,
  tx_id = NULL,
  exp = "all_merged-Homo_sapiens_modalities",
  libraries = NULL,
  leader_extension = 0,
  trailer_extension = 0,
  viewMode = FALSE,
  other_tx = FALSE,
  plot_on_start = TRUE,
  frames_type = "columns",
  kmer = 1,
  host = "https://ribocrypt.org"
)

Arguments

symbol	gene symbol, default NULL
gene_id	gene symbol, default NULL
tx_id	gene symbol, default NULL
exp	experiment name, default "all_merged-Homo_sapiens_modalities"
libraries	NULL, default to first in experiment, c("RFP","RNA") would add RNA to default.
leader_extension	integer, default 0. (How much to extend view upstream)
trailer_extension	integer, default 0. (How much to extend view downstream)
viewMode	FALSE (transcript view), TRUE gives genomic.
other_tx	FALSE, show all other annotation in region (isoforms etc.)
plot_on_start	logical, default TRUE. Plot gene when opening browser.
frames_type	"columns"
kmer	integer, default 1 (no binning), binning size of windows, to smear out the signal.
host	url, default "https://ribocrypt.org". Set to localhost for local version.

Value

character, URL.

Examples

make_rc_url("ATF4", "ENSG00000128272")

Miswi/RiboCrypt documentation built on Dec. 14, 2024, 10:37 p.m.