Query a MySQL Database from R using RMySQL

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -N \

 -e 'select concat("curl http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=",chrom,":",txStart-35,",",txStart-1) from knownGene where strand="+"'  |\

 sh > result.concatenated.xml

12345678910111213141516171819202122232425262728

#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