Mercurial > repos > elixir-it > vinyl_optimizer

comparison GENEO_VINYL.R @ 3:221db2eb3c8e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author elixir-it
date Wed, 22 Jul 2020 19:23:14 +0000
parents 6e4eb4856874
children
comparison
equal deleted inserted replaced
2:6e4eb4856874 3:221db2eb3c8e
50 m[,1]=c(posR,totR); 50 m[,1]=c(posR,totR);
51 m[,2]=c(posT,totT); 51 m[,2]=c(posT,totT);
52 52
53 F=fisher.test(m,alternative="greater") 53 F=fisher.test(m,alternative="greater")
54 Fpv=F$p.value 54 Fpv=F$p.value
55 Fodds=F$estimate 55 Fodds=F$estimate
56 localScore=0.5*-log10(Fpv)+0.3*Fodds-0.2*posT #+0.175*posR-0.125*posT 56 localScore=0.5*-log10(Fpv)+0.3*Fodds-0.2*posT #+0.175*posR-0.125*posT
57 if (localScore>score) 57 if (localScore>score)
58 { 58 {
59 59
60 score=localScore 60 score=localScore
66 } 66 }
67 67
68 } 68 }
69 Command=system("rm *.ofile *.ovcfile *.osummary",intern=FALSE) 69 Command=system("rm *.ofile *.ovcfile *.osummary",intern=FALSE)
70 outV=paste(round(x,digits=2),collapse="\t"); 70 outV=paste(round(x,digits=2),collapse="\t");
71 if (surv1>60)
72 {
73 surv1=62;
74 }
71 cat(paste(outV,surv1,totR,surv2,totT,pval,rat,score,"\n",sep="\t"),file=ofile,append=T); 75 cat(paste(outV,surv1,totR,surv2,totT,pval,rat,score,"\n",sep="\t"),file=ofile,append=T);
72 return(score*-1); 76 return(score*-1);
73 } 77 }
74 library(genalg) 78 library(genalg)
75 79
76 G=rbga(stringMin=minsV,stringMax=maxV,popSize=20,iters=25,evalFunc=evalVINYL) 80 G=rbga(stringMin=minsV,stringMax=maxV,popSize=50,iters=50,evalFunc=evalVINYL)
77 #cat(summary(G),file=ofile,append=T) 81 #cat(summary(G),file=ofile,append=T)
78