gene.track.view: Gene track visualization

In ccbiolab/svpluscnv: svpluscnv: analysis and visualization of complex structural variation data

Description

Creates a track visualization of a genomic region defined by gene boundaries or custom provided

Usage

gene.track.view(
  chrom = 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

chrom	(character) Chromosome (e.g. chr9)
start	(numeric) Genomic coordinate from specified chromosome to start plotting
stop	(numeric) Genomic coordinate from specified chromosome to stop 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	(character) Reference genome version to draw chromosome limits and centromeres (hg19 or hg38)
cex.text	(numeric) The magnification to be used for transcript RefSeq text added
addtext	(logic) Whether to include transcript RefSeq ids in the plot
plot	(logic) Whether to generate plot in open device
summary	(logic) Whether to produce a data.table output with transcript information
...	Additional graphical parameters

Value

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

Examples

# obtain the coordinates of a desired genomic regionbased on a known gene locus 
refSeqGene <- gene.symbol.info(refseq_hg19,"PTPRD")
chrom <- refSeqGene$chrom
start <- refSeqGene$start - 150000;
stop <- refSeqGene$stop + 50000;

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

ccbiolab/svpluscnv documentation built on Sept. 9, 2020, 4:52 a.m.