how to get fewer cut points with DNAcopy or GLAD
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Wittner, Ben ▴ 290
@wittner-ben-1031
Last seen 8.2 years ago
USA/Boston/Mass General Hospital
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 The information transmitted in this electronic communication...{{dropped}}
SNP affy DNAcopy GLAD SNP affy DNAcopy GLAD • 766 views
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