rmysql.r

rmysql.r

#Install the package if you've never done so
install.packages("RMySQL")

#Load the package
library(RMySQL)

# Set up a connection to your database management system.
# I'm using the public MySQL server for the UCSC genome browser (no password)
mychannel <- dbConnect(MySQL(), user="genome", host="genome-mysql.cse.ucsc.edu")

# Function to make it easier to query 
query <- function(...) dbGetQuery(mychannel, ...)

# Get the UCSC gene name, start and end sites for the first 10 genes on Chromosome 12
query("SELECT name, chrom, txStart, txEnd FROM mm9.knownGene WHERE chrom='chr12' LIMIT 10;")

# Results are returned as a data.frame:
#          name chrom txStart   txEnd
# 1  uc007mwj.2 chr12 3235525 3250374
# 2  uc007mwg.2 chr12 3235790 3239112
# 3  uc007mwh.2 chr12 3235790 3239288
# 4  uc007mwi.2 chr12 3235790 3250374
# 5  uc007mwk.1 chr12 3236610 3249997
# 6  uc011yjq.1 chr12 3237284 3241410
# 7  uc007mwl.2 chr12 3247427 3309969
# 8  uc007mwm.1 chr12 3365131 3406494
# 9  uc007mwn.1 chr12 3365131 3406494
# 10 uc007mwp.2 chr12 3403882 3426747