User: MatthewGField

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Posts by MatthewGField

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Answer: A: Calling amplifications and deletions from CopywriteR output
... Is there a way to extract calls (-2,-1,0,1,2) and segmented values directly from the segment.Rdata file, or do we have to go from the log2_read_counts.igv file?  I would like to create a heatmap of gains and losses across all the chromosomes of a bunch of samples combined.  Could you provide example ...
written 3.6 years ago by MatthewGField10
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Answer: A: Copywriter output looks strange
... Thomas Kuilman's response: You seem to suffer from a limited number of off-target reads (your MAD-value is quite high, your profile is rather vague and stripy (this comes from low count bins, which give rise to only a limited number of actual log2-values)). There are two things you could try: eithe ...
written 3.6 years ago by MatthewGField10
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Copywriter output looks strange
... I am very interested in using your CopywriteR technique to analyze gains and losses from exome data.  I went through the entire pipeline and have a very messy output. It does not look nearly as clean as the examples in the copywriter paper.  Am I supposed to interpret the green line at the top and ...
copywriter written 3.6 years ago by MatthewGField10

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