Package fork.lib.math.applied.stat

Examples of fork.lib.math.applied.stat.Distribution

50
51
52
53
54
55
56
57
58
59
60
61
62
    outNorm= new File(od+"/norm_"+f.getName());
}
   
   
public static void subtractBackground(Distribution dis, File f, File outSub, double rat)throws Exception {
    Distribution dislow= dis.subsetLowerThan(dis.quantileBoundaries(100).get(99));
    double med= dislow.median();
    double sd= dislow.standartDeviation();
    double thr= med+ sd* rat;
    System.out.println("med: "+ med+"   sd: "+ sd+"     trh:"+ thr);
   
   

View Full Code Here
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
}

public String getOutString(String li){
    String[] ns= li.split(",");
    String out= "c(";
    Distribution dis= new Distribution();
    for(int i=0; i<ns.length ; i++){
        String n= ns[i];
        if(tfb.containsKey(n)){
            String ss= tfb.get(n);
            out+=ss+",";
            dis.add(Integer.parseInt(ss));
        }
    }
    out= out.substring(0, out.length()-1);
    out+=")";
    out+="\nmu:"+dis.mean()+"   zero:"+ (double)dis.subsetLowerOrEqualTo(0).size()/dis.size()
            +"  me:"+dis.median()+"   s:"+dis.standartDeviation();
    return out;
}
View Full Code Here
37
38
39
40
41
42
43
44
45
46
47
48
49
50
   
   

   
protected void init() throws Exception{
    Distribution disall= new Distribution(gvs.values());
    Distribution dis= disall.subsetHigherThan(0);
   
    ArrayList<Double> bs= dis.quantileBoundaries(intv);
    bs.add(0, -0.1);
   
    for( int i=0; i<bs.size()-1 ; i++ ){
        String n = tit+i+"_"+bs.get(i)+"_"+bs.get(i+1);
        sets.add(new GeneSet(n));
View Full Code Here
48
49
50
51
52
53
54
55
56
57
58
    public void init() throws Exception{
        ArrayList<Double> vs= new ArrayList<>();
        for(int i=0; i<vss.length ; i++){
            vs.add( vss[i][col] );
        }
        double thr= new Distribution(vs).quantileBoundaries(20).get(1);
        String thrs= new DecimalFormat("0.##E0").format(thr);
       
        sets.add(new GeneSet(tit+"_"+thrs+"_y"));
        sets.add(new GeneSet(tit+"_"+thrs+"_n"));
       
View Full Code Here
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
   
   


public static void normalise(LandscapeBuilder lb, File f, String tit) throws Exception{
    Distribution d= lb.getDistribution();
    double fac= (double)Math.ceil( d.median() * 1.75);
    new LandscapeTransformer(lb).subtract(fac);
    System.out.println("subfac: "+fac);
   
    Distribution dnz= lb.getDistributionNonZero();
    double nf= dnz.sum()/ 100000000;
    new LandscapeTransformer(lb).divideBy(nf);
    BedGraphExporter be= new BedGraphExporter(lb);
    be.param().tit= tit;
    be.writeToFile(f);
}
View Full Code Here
52
53
54
55
56
57
58
59
60
61
62
protected void random()throws Exception {
   
    System.out.println(ovl(gbtar, gbref));
   
    Distribution disb= new Distribution();
    //for( int i=0; i<100; i++ ){
    for( int i=0; i<1; i++ ){
        FrequencyCount<Integer> lens= gbtar.lengthDistribution();
        //System.out.print(i+"    ");
       
View Full Code Here
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
    NormChipSeqRPM.toRatio(f, in, outRat);
}

public void subtract()throws Exception {
   
    Distribution dis0 = new BedGraphBuffer(outRat).getDistributionNonZero();
    Distribution dis= dis0.subsetHigherThan(1);
    dis= dis.subsetLowerOrEqualTo(dis.quantileBoundaries(10).get(5));
   
   
    double mean= dis.mean();
    double sd= dis.standartDeviation();
    double rat= mean+ 1.2 *sd;
   
    System.out.println("m: "+ mean+"   sd: "+sd+"  rat: "+rat);
   
    //double rat= 2.5;
View Full Code Here
125
126
127
128
129
130
131
132
133
134
135
136
137
138


   
public void subtract2()throws Exception {
    Distribution dis= new BedGraphBuffer(outSub).getDistributionNonZero();
    dis= dis.subsetLowerThan(dis.quantileBoundaries(10).get(7));
    double med= dis.median();
    double sd= dis.standartDeviation();
    double thr= med+ sd* 2;
    System.out.println("med: "+ med+"   sd: "+ sd+"     "+ thr);

    BufferedWriter bw= new BufferedWriter(new FileWriter(outSub2));
    BedGraphExporter.writeTitle(bw, FileName.getBaseName(outSub2));
View Full Code Here
61
62
63
64
65
66
67
68
69
70
71
72
73
            LandscapeScoring ls= new LandscapeScoring(lb, gb){
                protected double[] score(ArrayList<Region> bufs, GenomicRegion gr) throws RegionException{
                    return new double[]{Landscape2DBuffer.getArea(bufs, gr), gr.getRange()+1 };
                }
            };
            Distribution dis= LandscapeScoringResultEntry.toDistribution(ls.getResultEntries(), 0);
            lens.add(LandscapeScoringResultEntry.toDistribution(ls.getResultEntries(), 1).sum());
            double s= dis.sum();
            vs.add(s); sum+=s;
            //LandscapeScoringResultEntry.writeToFile(ls.getResultEntries(), new File(out.getParentFile()+"/file_"+f.getName()) );
        }
    }
    BufferedWriter bw= new BufferedWriter(new FileWriter(out));
View Full Code Here
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41



public void init(LandscapeBuilder lb) throws Exception{
    Distribution d= lb.getDistributionNonZero();
    ArrayList<Double> qs= d.quantileBoundaries(100);
    double m=0 ,sd=0;
    for( int i=0; i<50; i++ ){
        Distribution df= d.subset(qs.get(i), qs.get(qs.size()-1-i), true, true);
        m= df.mean();
        sd= df.standartDeviation();
        double z= sd/m;
        //System.out.println(i+"   mean: "+m+"   med: "+med+"   sd: "+ sd+"  z:"+z);
        if(z<0.2){
            break;
        }
View Full Code Here
TOP

Related Classes of fork.lib.math.applied.stat.Distribution

  • common.inspect.ClassifierGeneValue
  • common.TFBinding
  • data.cerevisiae.harbison.Harbison2004L$HClassifier
  • data.cerevisiae.inhouse.a_norm.NormChipChip
  • data.cerevisiae.inhouse.a_norm.NormChipSeqRPM
  • data.cerevisiae.inhouse.a_norm.NormChipSeqZero
  • data.cerevisiae.inhouse.a_norm.NormRNASeq
  • data.cerevisiae.inhouse.a_score.ScoreOverviewSet
  • data.human.inhouse.norm.NormChipSeq
  • data.human.statham2014mods.InspectCrossover
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.