fix output (segmented, focal, proper GISTIC), include X/Y, add GISTIC-like example, fix saveRDS#18
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ttriche wants to merge 11 commits intohovestadtlab:mainfrom
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fix output (segmented, focal, proper GISTIC), include X/Y, add GISTIC-like example, fix saveRDS#18ttriche wants to merge 11 commits intohovestadtlab:mainfrom
saveRDS#18ttriche wants to merge 11 commits intohovestadtlab:mainfrom
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nb. the output now correctly retains X and Y aberrations for GISTIC and CNVRanger, which is good, because these are the most common recurrent alterations in leukemia and any caller that misses them is automatically wrong |
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one of the reasons to document ALL relevant, valid inputs to a function is that these corner cases may be important... ! |
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nb. the "conflicts" to be resolved are methods for these fix issue #20 |
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saveRDS
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the output code was pretty janky, so I refactored it. this helped enormously with getting usable output.
fixes issue #17
also fixes issue #19
also fixes issue #20