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

Description Usage Arguments Value Examples

View source: R/gene.track.view.r

Description

Plot genome tracks in local genomic regions

Usage

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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

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

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