plot.genes: Plot genes provided in a bed file
In cgmisc-team/cgmisc: Various functions useful in computational genetics, e.g. in GWAS

plot.genes

R 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).