search for: chromstart

...[i-1,6]+1) x<-as.numeric(all.tf7[i,2]) } else if (all.tf7[i,1]!=all.tf7[i-1,1]) { all.tf7[i,6]<-(all.tf7[i-1,6]+1) x<-as.numeric(all.tf7[i,2]) } } #the aim here is to attribute a bin number to each row so that I can then split the dataframe according to those bins. chrom chromStart chromEnd name cumsum bin chr1 10089 10309 ZBTB33 10089 1 chr1 10132 10536 TAF7_(SQ-8) 20221 1 chr1 10133 10362 Pol2-4H8 30354 1 chr1 10148 10418 MafF_(M8194) 40502 1 chr1 1038...

...BI Loading required package: gsubfn Loading required package: proto Loading required namespace: tcltk Loading Tcl/Tk interface ... done Loading required package: chron Loading required package: RSQLite Loading required package: RSQLite.extfuns > result<-sqldf("select data.*, meth450part.chromStart as MethChromStart, meth450part.chromEnd as MethChromEnd, meth450part.strand as MethStrand, meth450part.name as MethName, meth450part.score as MethScore from data join meth450part where data.V1=meth450part.chrom and data.V2<=meth450part.chromStart and data.V3>=meth450part.chromEnd") L...

Bruce Pennypacker wrote that he was having a problem using the R library sqldf under Red Hat 5.6: > library("sqldf") .. > result<-sqldf("select data.*, meth450part.chromStart as MethChromStart, meth450part.chromEnd as MethChromEnd, meth450part.strand as MethStrand, meth450part.name as MethName, meth450part.score as MethScore from data join meth450part where data.V1=meth450part.chrom and data.V2<=meth450part.chromStart and data.V3>=meth450part.chromEnd") Loadi...

I am running a simple SQL SELECT statement that involvs 50k + data points using R and the RJDBC interface. I am facing very slow response times in both the RGUI and the R console. When running this SQL statement directly in a SQL client I have processing times that are a lot lot faster (which means that the SQL statement itself is not the problem). Did any of you compare RJDBC vs RMySQL or is