plot.genes: Plot genes provided in a bed file

View source: R/plot.genes.R

plot.genesR Documentation

Plot genes provided in a bed file

Description

Using information provided in a bed file, plot genes, together with their names and strand information.

Usage

plot.genes(region, chr, bed.path = NULL)

Arguments

region

IRanges

bed.path

is a path to a bed file containing gene information.

Details

When using UCSC-provided bigBed annotation files you need to first use the bigBedToBed tool (available from: http://hgdownload.cse.ucsc.edu/admin/exe/YOUR_OS_DIRECTORY) to get the right format. At this point you can also extract the desired chromosome. Then you need to strip the last column of the bed file using, for instance awk: awk 'out=""; for(i=1;i<=15;i++)out=out" "$i; print out' my.bed > myFinal.bed Here, we provide a Broad Improved Canine Annotation v.1 protein coding genes for the canine chromosome 2 (see: https://www.broadinstitute.org/ftp/pub/vgb/dog/trackHub/hub.txt).

Value

ggplot2 plot

Author(s)

Veronika Scholz <veronikascholz@gmail.com>


cgmisc-team/cgmisc documentation built on Jan. 3, 2024, 9:52 p.m.