igv.loci: igv.loci Wrapper for igv function to dump table + screenshots...

In mskilab/skitools: Various mskilab R utilties

igv.loci Wrapper for igv function to dump table + screenshots for individual GRanges loci that have sample column (default Tumor_Sample_Barcode) that is a key into ind data.table where columns matching col.string are fetched and plotted IGV host and port are taken from environment variables

Description

Wrapper for igv function to visualize a given (single) mutation in a maf file

Usage

igv.loci(
  mut,
  ind,
  out.path,
  sample.key = "Tumor_Sample_Barcode",
  sleep = 30,
  window = 400,
  host = Sys.getenv("IGV_HOST"),
  port = Sys.getenv("IGV_PORT"),
  overwrite = FALSE,
  snapshots = TRUE,
  verbose = TRUE
)

Author(s)

Marcin Imielinski

mskilab/skitools documentation built on March 5, 2025, 11:52 p.m.