Genomic coordinates for Cytogenetic bands with R

Question

[zlskidmore]

Hi All,

Does anyone know of a resource in R to obtain the genomic coordinates of cytogenetic bands. I have tried bioMart without success and was hoping to obtain this information through an R interface without resorting to an outside resource.

Answer 1

[Alex Reynolds]

You could probably run the following command-line search via a system() or MySQL library call within R:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e "SELECT chrom, chromStart, chromEnd, name FROM cytoBand"

For instance:

> result <- system("mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e \"SELECT chrom, chromStart, chromEnd, name FROM cytoBand\"", intern=TRUE)

Or you might run the RMySQL library:

> install.packages("RMySQL", type="source")
> library(RMySQL)
> connection <- dbConnect(MySQL(), user="genome", host="genome-mysql.cse.ucsc.edu", dbname="hg19")
> result <- dbGetQuery(conn=connection, statement="SELECT chrom, chromStart, chromEnd, name FROM cytoBand")

The output from system() may require additional parsing with split() and other functions to build a matrix or data frame.

[zlskidmore]

Thanks Alex,

did not realize R could connect to an SQL database

Answer 2

[Julian Gehring]

You can use the getIdeogram function from the biovizBase package which will query UCSC for you. As an example, get the cytobands for the human hg19 genome:

library(biovizBase)
hg19IdeogramCyto <- getIdeogram("hg19", cytobands = TRUE)

This will work for all genomes and species that are provided by UCSC.