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Wave Detection and Correction

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7.14 Wave Detection and Correction

Some samples in copy number datasets may suffer from genomic waves, which cause the Log R Ratios to drift up or down in a wave-like fashion. SVS uses the method described in [Diskin 2008] to detect and partially correct for this phenomenon.

Wave Detection

The Wave Factor score is a metric for evaluating the severity of this phenomenon in a sample. SVS Wave Detection computes the absolute value of the Wave Factor for each sample. The GC content in the region around each marker is thought to contribute to the genomic wave phenomenon, so SVS also computes the correlation coefficient between the Log R Values and the GC content around each marker. After performing wave detection, a spreadsheet will be created containing the Abs. Wave Factor and GC Correlation for every sample.

Wave Correction

Optionally, SVS can use the GC correlation to correct for the waviness contributed by GC content. This will produce a new spreadsheet with the same row and column labels as the input that contains corrected log ratios for every sample.

Options
Min Training Marker Distance
When computing the GC correlation, only a subset of available markers are used that will be spaced at least this many Kilobase pairs apart. This avoids biasing the correlation towards regions with high marker density.
GC Reference
It is not necessary to manually calculate the GC content around each marker in your dataset. SVS will use the specified reference genome to automatically compute the GC percentage in the 1 megabase region around each marker.
Chromosome Selection
If Autosomes Only is selected, only chromosomes with a numeric name(eg. “1”, “15”, “22”) will be used for wave detection/correction. If All Chromosomes is selected, then every active chromosome in the spreadsheet will be used.
Output
If Detect Only is selected, A new spreadsheet containing the Abs. Wave Factor and GC correlation will be created. Detect and Correct will also produce a new spreadsheet containing corrected Log R Ratios.

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