HotspotsCNV: HotspotsCNV
In mbertalan/iPsychCNV: iPsychCNV

Description Usage Arguments Details Value Author(s) Source Examples

HotspotsCNV: Identify Copy Number Variation (CNV) hotspots.

1 2	HotspotsCNV(df, Freq = 1, OverlapCutoff = 0.7, Cores = 1, OverlapMin = 0.9, OverlapMax = 1.1, hg = "hg19")

`Df:`	Dataframe with CNV predction with chromosome (Chr.), start, and stop position.
`Freq:`	Minimum number of CNVs to be considered a hotspot, default = 1.
`OverlapCutoff:`	Minimum overlap among CNVs to be considered the same CNV region, default = 0.7.
`Cores:`	Numeric, Number of cores used, default = 1.
`OverlapMin:`	Minimum overlap with hotspot to be selected for counting, default = 0.9.
`OverlapMax:`	Maximum overlap with hotspot to be selected for counting, default = 1.1.
`hg:`	Human genome version, default = hg19. For full range of possibilities, run ucscGenomes()$db rtracklayer

Specifically designed to handle noisy data from amplified DNA on phenylketonuria (PKU) cards. The function is a pipeline using many subfunctions.

CNV hotspots.

Marcelo Bertalan, Louise K. Hoeffding, Ida Elken Sønderby.

http://biopsych.dk/iPsychCNV

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MockDataCNVs <- MockData(N=100, Type="PKU", Cores=20)
iPsych.Pred <- iPsychCNV(PathRawData=".", MINNumSNPs=20, Cores=20, Pattern="^MockSample", MinLength=10, Skip=0)
iPsych.Pred.hotspots <- HotspotsCNV(iPsych.Pred, Freq=2, OverlapCutoff=0.9, Cores=1)