Examples of PeakIdentifier

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

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        this.lb=lb;
    }
   
   
public void writeToFile(File out)throws Exception {
    PeakIdentifier pi= new PeakIdentifier(lb, null);
    pi.param().joinGap=150;
    GenomicRegionsBuilder gb= pi.getPeaks();
    new BedExporter(gb).writeToFile(out);
}
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Examples of fork.lib.bio.anno.genomic.PeakIdentifier

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    LandscapeTransformer lt= new LandscapeTransformer(lb);
    lt.subtract(10);
   
   
    PeakIdentifier pi= new PeakIdentifier(lb, null);
    pi.getPeaks().writeToFileBed(new File("peak_"+FileName.getBaseName(f)+".bed"));
   
}
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Examples of fork.lib.bio.anno.genomic.PeakIdentifier

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    File f= new File(dir+"/data/chip-seq/norm/norm_wig_chip_htz1-anti660_772-wt_sd_20131104-r1_pe1_sacCer1.wig");
    File od= new File(dir+"/data/chip-seq/norm/peak3");
   
   
    LandscapeBuilder lb= new BedGraphReader(f).getLandscapeBuilder();
    PeakIdentifier pi= new PeakIdentifier(lb, null);
   
    pi.getPeaks().writeToFileBed(new File(od+"/peak_"+FileName.getBaseName(f)+".bed"));
   
   
   
}   
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