plotGenes: Plot genes from a specified region of the human genome.

In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

Plot genes from a specified region of the human genome.

Description

Retrieves genes from the UCSC Genome Browser and generate the genes plot.

Usage

plotGenes(minRange, maxRange, chromosome, genome = "hg19", plot_lines_distance = 0.03,
vp = viewport(x = 0, y = 0.99, just = c("left", "top")), splice_variants = TRUE,
non_coding = TRUE)

Arguments

minRange	The sequence minimum range in base pairs.
maxRange	The sequence maximum range in base pairs.
chromosome	A character string identifying the chromosome.
genome	The genome assembly to use. The default is hg19, the most recent human genome assembly on the UCSC genome browser.
plot_lines_distance	The distance between the lines of genes plotted.
vp	A viewport.
splice_variants	If FALSE, exclude gene splice variants.
non_coding	If FALSE, exclude non-coding genes.

Details

The genes are color coded as follows: Black – feature has a corresponding entry in the Protein Data Bank (PDB) Dark blue – transcript has been reviewed or validated by either the RefSeq, SwissProt or CCDS staff Medium blue – other RefSeq transcripts Light blue – non-RefSeq transcripts

For assemblies older than hg18, all genes are plotted in grey.

Value

A grob of gene plots.

Author(s)

Sigal Blay <[e-mail]> and more

References

http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene

Examples

## Not run: 
grid.newpage()
plotGenes(149500000, 150000000, "chr7")

## End(Not run)

GabrielHoffman/decorate documentation built on May 23, 2023, 1:29 a.m.