[BioC] how to get fewer cut points with DNAcopy or GLAD

[Wittner, Ben, Ph.D.]

I've been attempting to use segment() in DNAcopy or glad() in GLAD to segment
copy-number data from Affy 500K SNP chips.

My problem is that both of those functions find tens of thousands of
segmentation points, whereas I would like them to find at most tens of
segmentation points.

I tried lowering the alpha argument to DNAcopy's segment(), but even lowering it
by 3 orders of magnitude only lowered the number of segments found by a factor
of 2.

Any suggestions would be appreciated.

BTW, before submitting the log ratios to segment() and glad(), I median filter
them using a window size of 9. I'm hesitant to use a bigger window size for fear
of loosing spatial resolution in my eventual findings.

Thanks.

-Ben


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