writeIgvSession: Writes an IGV session

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

Writes an IGV session

Description

Writes an IGV session into a separate .xml file

Usage

getIgvGenome(param)

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

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.

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.

• writeIgvSessionLink(): Writes an IGV session link.

Author(s)

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 5, 2025, 3:41 p.m.