writeIgvSession: Writes a jnlp link to a static html

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

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 Dec. 26, 2024, 9:53 a.m.