V15 Fix molecular-subtype-chordoma analysis #590
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@jaclyn-taroni I have two fix ideas for the lack of chordoma samples in subset for this notebook.
At this point in time, we are thinking 2 would be okay, but I wanna clear it by you before I implement it. |
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There is another option - have the first step of this module be it’s own subsetting where all resulting files are committed to the repository. That is what we do for other subtyping modules. |
I was just noticing this for the other subtyping modules. I will try to follow their suit then. |
analyses/molecular-subtyping-chordoma/00-subset-files-for-chordoma.R
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analyses/molecular-subtyping-chordoma/00-subset-files-for-chordoma.R
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This reverts commit 400be46.
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Meant to leave that comment in the main thread... |
| ``` | ||
| This bash script the same regardless of where it is called and will first subset the data to `Chordoma` samples |
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Looks like you're missing a verb here, correct?
| # Subset metadata | ||
| subset_metadata <- histologies_df %>% | ||
| dplyr::filter(short_histology == "Chordoma") %>% | ||
| select( |
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You're calling the filter function above using dplyr:: but not doing the same for select here. Is this because filter was behaving similarly to rename as you noted in your original comment? If so, then disregard this comment. If not, removing the dplyr:: altogether (except for in the case of the rename function) or adding the dplyr:: to the rest of the functions would be nice for consistency purposes.
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filter also has a base:: function that can mess with stuff sometimes.
| # remove large expression matrix that's no longer needed | ||
| rm(expression_data) | ||
| # now only the columns correspond to chordoma samples | ||
| smarcb1_expression <- smarcb1_expression[, which(colnames(subset_expression_data) %in% subset_metadata$Kids_First_Biospecimen_ID) ] |
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This line looks weird (format-wise), did you run this through a styler?
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I did but it doesn't do anything with really long lines. I'd rather use dplyr::filter here anyway but was trying to keep the original code here.
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Merging before expected CI failure. |
Purpose/implementation Section
There are not enough chordoma samples in the subset CircleCI files to test so I switched to the approach that was used in the other subtyping modules.
Looks like the
renamesteps were not working because of library load and it was not calling thedplyr::renamebut anotherrename. So to fix I added a series ofdplyr::, reran the notebook with v15 and pushed the results.What GitHub issue does your pull request address?
#574
Reproducibility Checklist
These items were all taken care of previously.
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.