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Use ploidy for copy.num when running GISTIC #1400
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sjspielman
reviewed
May 20, 2022
| dplyr::select(Kids_First_Biospecimen_ID, tumor_ploidy) %>% | ||
| dplyr::rename(ID = Kids_First_Biospecimen_ID) %>% | ||
| dplyr::inner_join(cnv_consensus, by="ID") %>% | ||
| dplyr::mutate(copy.num = dplyr::case_when(is.na(copy.num) ~ tumor_ploidy, TRUE ~ copy.num)) %>% |
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Spacing for clarity (though the spacing doesn't come out well in the github suggestion..)
Noting that one could recreationally revise this to be ifelse(), or one could leave it as is.
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| dplyr::mutate(copy.num = dplyr::case_when(is.na(copy.num) ~ tumor_ploidy, TRUE ~ copy.num)) %>% | |
| dplyr::mutate(copy.num = dplyr::case_when( | |
| is.na(copy.num) ~ tumor_ploidy, | |
| TRUE ~ copy.num)) %>% |
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I recreationally moved this Rscript so it gets checked in CI to boot!
sjspielman
approved these changes
May 20, 2022
Co-authored-by: Stephanie <stephanie.spielman@gmail.com>
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Purpose/implementation Section
Closes #1180 using the same solution as d3b-center#119
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.