The software is devoted to discover aberration in copy number (CNA) of genomic data. The CNA loci are found by applying a batch of significance test to data obtained by arrays of Comparative Genomic hybridization (aCGH) technology. The test statistic used is a sum of Bernoulli trials with different parameter. The sampling distribution of the test statistic under the null hypothesis is approximated by a shuffling scheme devised by the permutation test methodology. A further p-value corrections for multiple test allows to prevent from false discovery. The algorithm provide a good behavior both in real and synthetic data.
GAIA: an R/Bioconductor package for identification of significant genetic mutations from multiple samples
PAGNOTTA S;CECCARELLI M;
2010-01-01
Abstract
The software is devoted to discover aberration in copy number (CNA) of genomic data. The CNA loci are found by applying a batch of significance test to data obtained by arrays of Comparative Genomic hybridization (aCGH) technology. The test statistic used is a sum of Bernoulli trials with different parameter. The sampling distribution of the test statistic under the null hypothesis is approximated by a shuffling scheme devised by the permutation test methodology. A further p-value corrections for multiple test allows to prevent from false discovery. The algorithm provide a good behavior both in real and synthetic data.| File | Dimensione | Formato | |
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GAIA_Bioconductor.pdf
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GAIA_Bioinformatics.pdf
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