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NCBI-Hackathons / Scan2CNV

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CNV caller: DNAcopy #39

Open ngiangre opened 7 years ago

ngiangre commented 7 years ago

These functions are used extensively by gsrc and other packages

http://bioconductor.org/packages/release/bioc/html/DNAcopy.html

ngiangre commented 7 years ago

faster implementation

http://bioconductor.org/packages/release/bioc/html/fastseg.html

ngiangre commented 7 years ago

I'm trying to see if there's any pre-processing. It seems that they just require the log ratio of red and green for each marker. They recommend a "smoothing" beforehand but that's fortran wrapped up. I presume they do segmentation by consistent log ratios across markers but it isn't clear. Seems like it gives useful visualizations. https://www.bioconductor.org/packages/release/bioc/vignettes/fastseg/inst/doc/fastseg.pdf