Update get_ssm_by_region - #15
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rdmorin
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rdmorin
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A few things need to be clarified in the comments and I highlighted one potential problem in the test outputs.
| 6: 8 127721754 127721755 14 105863234 105863235 . 112 - + BLGSP-71-08-00023-01A-01D MYC IGH IGH-MYC | ||
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| > table(annotated_myc_hg38$partner) | ||
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Do we know what caused this change? Looks problematic.
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The function get_manta_sv uses GAMBLR.data::sample_data[[projection]]$bedpe which was last changed on June 30, 2025. The log file has not been changed since Mar 29, 2025. That is my best guess as to where these changes are coming from -- the .rda have been updated. The other source of the changes could be the samples returned by get_gambl_metadata since it uses GAMBLR.data::sample_data$meta. So likely the data has been changed since the last commit of this log output, but I can't be 100% sure.
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When there is a major revision to the data objects, like in morinlab/GAMBLR.data#122, should re-run certain log scripts be done as part of that? e.g. log scripts for .open and .viz in particular
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Describe your changes
Addresses
get_ssm_by_regionsto take MAF data #14Related issues in other child packages
ashm_rainbow_plotGAMBLR.results#118ashm_rainbow_plotandashm_multi_rainbow_plotGAMBLR.viz#128Indicate which issue(s) this addresses, if applicable
Checklist before requesting a review
GAMBLR_examples_output.login my pull request and confirm the changes to this file are expected