add CN for unmatched samples #3
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rdmorin
requested changes
May 15, 2021
| as.data.frame() %>% | ||
| dplyr::filter(! ID %in% all_segs_matched$ID) | ||
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| all_segs = rbind(all_segs_matched, |
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I have a suggestion. Can you add a column to the data frame before merging it and populate it with the tool name so it would look something like this after rbind? (showing toy example with one row from each tool)
ID chr start end LOH_flag log.ratio method
something chr1 1 100000 0 0 battenberg
somethingelse chr1 1 1203000 0 0 controlfreec
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You'll just need to check some of the other functions that use this function to make sure it doesn't break anything
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I have annotated the method, tested with downstream functions, and pushed the update
rdmorin
approved these changes
May 16, 2021
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For unmatched samples where battenberg results are not available, results from controlfreec will be used instead. It pulls all controlfreec results during mysql qery into a separate dataframe, and in a pipe filters out samples that already have battenberg results. Then, 2 data frame are merged together.