Package fork.lib.bio.anno.genomic

Examples of fork.lib.bio.anno.genomic.LandscapeTransformer.divideBy()

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    LandscapeBuilder lb= new BedGraphReader(outSub).getLandscapeBuilder();
    LandscapeTransformer lt= new LandscapeTransformer(lb);
    lt.selectLength(300, Integer.MAX_VALUE);
    double sum= lb.totalArea();
    double fac= sum/Math.pow(10, 8);
    lt.divideBy( fac );
    new BedGraphExporter(lb).writeToFile(outNorm);
}
   
public void subtract()throws Exception {
    subtractBackground(dis, f, outSub, 4);
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public void writeToDir(File od)throws Exception {
    double sum = lbf.totalArea()+ lbr.totalArea();
    double fac= sum/ Math.pow(10, 10);
    LandscapeTransformer ltf= new LandscapeTransformer(lbf);
    ltf.divideBy(fac);
    new BedGraphExporter(lbf).writeToFile(new File(od+"/norm_"+tag+"_for.wig"));
    LandscapeTransformer ltr= new LandscapeTransformer(lbr);
    ltr.divideBy(fac);
    new BedGraphExporter(lbr).writeToFile(new File(od+"/norm_"+tag+"_rev.wig"));
}
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    double fac= sum/ Math.pow(10, 10);
    LandscapeTransformer ltf= new LandscapeTransformer(lbf);
    ltf.divideBy(fac);
    new BedGraphExporter(lbf).writeToFile(new File(od+"/norm_"+tag+"_for.wig"));
    LandscapeTransformer ltr= new LandscapeTransformer(lbr);
    ltr.divideBy(fac);
    new BedGraphExporter(lbr).writeToFile(new File(od+"/norm_"+tag+"_rev.wig"));
}
   

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    LandscapeBuilder lb= new BedGraphReader(outSub2).getLandscapeBuilder();
    LandscapeTransformer lt= new LandscapeTransformer(lb);
    lt.selectLength(150, Integer.MAX_VALUE);
    double sum= lb.totalArea();
    double fac= sum/Math.pow(10, 8);
    lt.divideBy( fac );
    new BedGraphExporter(lb).writeToFile(out);
}
   

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