gene.track.view: Plot genome tracks in local genomic regions

In gonzolgarcia/svcnvplus: Integrative analyses of CNV segmentation and SV variant calls

Description

Plot genome tracks in local genomic regions

Usage

gene.track.view(
  chr = NULL,
  start = NULL,
  stop = NULL,
  symbol = NULL,
  upstr = NULL,
  dnstr = NULL,
  genome.v = "hg19",
  cex.text = 0.6,
  addtext = TRUE,
  plot = TRUE,
  summary = TRUE,
  ...
)

Arguments

chr	(character) chromosome (e.g chr9)
start	(numeric) genomic coordinate from specified chromosome to start plotting
symbol	(character) gene acceoted hgnc symbol to retrieve coordinates and area plotting ()
upstr	(numeric) distance upstream specified gene to extend the area plotted
dnstr	(numeric) distance downstream specified gene to extend the area plotted
genome.v	(hg19 or hg38) reference genome version to draw chromosome limits and centromeres
addtext	(logic)
plot	(logic)
summary	(logic) whether the function shoud return CNV segment 'segbrk' and SV 'svbrk' breakpoints tabular output
...	additional plot parameters from graphics plot function
end	(numeric) genomic coordinate from specified chromosome to stop plotting
addlegend	(logic)

Value

a data.frame with gene isoform annotations and/or plot into open device

Examples

gene.track.view(symbol="PTPRD", genome.v="hg19")

gonzolgarcia/svcnvplus documentation built on March 4, 2020, 6:02 p.m.