writeIgvSession: Writes a jnlp link to a static html

View source: R/igv.R

writeIgvSessionR Documentation

Writes a jnlp link to a static html

Description

Writes a jnlp link to a static html. The html can be moved as long as the session xml stays in the same directory.

Writes an IGV session into a separate .xml file

Usage

writeIgvSession(
  genome,
  refBuild,
  file = "igvSession.xml",
  bamUrls = NULL,
  vcfUrls = NULL,
  locus = "All"
)

getIgvGenome(param)

addIgvSessionLink(
  genome,
  refBuild,
  bamFiles,
  doc,
  locus = "All",
  label = "Open Integrative Genomics Viewer",
  baseUrl = PROJECT_BASE_URL
)

writeIgvSessionLink(
  genome,
  refBuild,
  bamFiles,
  html,
  locus = "All",
  label = "Open Integrative Genomics Viewer",
  baseUrl = PROJECT_BASE_URL
)

Arguments

genome

a character representing the build name.

refBuild

a character representing a file path to the reference build.

file

a character representing the name of the file to write the IGV session in.

bamUrls

a character vector containing BAM file links.

vcfUrls

a character vector containing VCF file links.

locus

a character describing which loci were used.

html

a character representing an html address.

htmlFile

a character, ending with .html, representing the file path of an html file.

projectId

a character representing the project ID.

Value

Returns a character containing the name of the newly written .xml file.

Functions

  • getIgvGenome: Gets the IGV genome if specified or otherwise tries to get the build name from the parameters.

  • addIgvSessionLink: Adds an IGV session link to an object of the class bsdoc.

  • writeIgvSessionLink: Writes an IGV session link.

Author(s)

Rehrauer, Hubert

Schmid, Peter

Rehrauer, Hubert

Schmid, Peter

See Also

newXMLNode

saveXML

addChildren

Examples

param = ezParam()
genome = getIgvGenome(param)
writeIgvSession(genome, param$ezRef["refBuild"])

uzh/ezRun documentation built on March 28, 2024, 8:44 a.m.