Package fork.lib.bio.anno.genomic

Examples of fork.lib.bio.anno.genomic.LandscapeComparatorBuffer

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public static void toDiff(File f, File ref, File out) throws Exception{
    LandscapeBuffer lb= new BedGraphBuffer(f);
    LandscapeBuffer lbref= new BedGraphBuffer(ref);

    LandscapeComparatorBuffer lc = new LandscapeComparatorBuffer(lb, lbref) {
            @Override
            public double newValue(double v, double refv) {
                return new Double( (double)Math.round( (v- refv) * 1000)/1000  );
            }
        };
    String tag= FileName.getBaseName(f);
    lc.writeToFile(out, "diff"+tag);
}
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public void writeToFile(File out)throws Exception{
    out.getParentFile().mkdirs();
    LandscapeBuffer lb= new BedGraphBuffer(f);
    LandscapeComparatorBuffer lc = new LandscapeComparatorBuffer(lb, lbref) {
            @Override
            public double newValue(double v, double refv) {
                if(refv<0.01){
                    refv=0.01;
                }
                return new Double( (double)Math.round(v/refv * 1000)/1000  );
            }
        };
    String tag= FileName.getBaseName(f)+"_lee2007";
    System.out.println("write ratio to: "+out);
    lc.writeToFile(out, "ratio_"+tag);
}
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}


public static void subtract( LandscapeBuffer lbf, LandscapeBuffer lbfref,
        File f, String tit, final double depthFactor) throws Exception{
    LandscapeComparatorBuffer lc= new LandscapeComparatorBuffer(lbf, lbfref) {
            @Override
            public double newValue(double v, double refv) {
                double ret= (double)Math.round( (v- refv*depthFactor) *100)/100;
                if(ret<0){
                    ret=0;
                }
                return ret;
            }
        };
    lc.writeToFile(f, tit);
}
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public static void toRatio(File f, File ref, File out) throws Exception{
    LandscapeBuffer lb= new BedGraphBuffer(f);
    LandscapeBuffer lbref= new BedGraphBuffer(ref);

    LandscapeComparatorBuffer lc = new LandscapeComparatorBuffer(lb, lbref) {
            @Override
            public double newValue(double v, double refv) {
                return new Double( (double)Math.round(v/refv * 1000)/1000  );
            }
        };
    String tag= FileName.getBaseName(f);
    System.out.println("write ratio to: "+out);
    lc.writeToFile(out, "ratio"+tag);
}
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Related Classes of fork.lib.bio.anno.genomic.LandscapeComparatorBuffer

  • data.cerevisiae.inhouse.a_norm.NormChipSeqRPM
  • data.cerevisiae.lee2007.NormToLee
  • data.cerevisiae.test.ratio.ToRatio
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