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Genomic coordinates for Cytogenetic bands with R

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.

r ideogram
• 4,667 views • link
updated by Ram Ram • written by zlskidmore zlskidmore

2 answers

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.

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updated by Ram Ram • written by Alex Reynolds Alex Reynolds

Thanks Alex,

did not realize R could connect to an SQL database

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written by zlskidmore zlskidmore

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.

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updated by Ram Ram • written by Julian Gehring • Julian Gehring

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