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Update fusion-summary to include union of biospecimen IDs in fusion callers #478
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Change to notebook for documentation purposes
Also +x
To better match former behavior
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jashapiro
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| prepareOutput <- function(fuseDF, bioid) { | ||
| fuseDF %>% | ||
| reshape2::dcast(Sample ~ FusionName) %>% | ||
| bind_rows(data.frame(Sample = setdiff(bioid, fuseDF$Sample))) %>% |
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This would be the same, correct?
right_join(data.frame(Sample = bioid)) %>%
jashapiro
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Co-Authored-By: jashapiro <jashapiro@gmail.com>
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* Make wording consistent, rerun * Add notebook for combining CN, mutation data * Add notebook to shell script * Rename to reflect change in purpose * WIP: adding RNA data * Fleshed out HGG subtyping notebook * Fix notebook name in shell script * Change broad and short histology columns * HGG -> DMG * Rerun subsetting step Changes appear to be related to removal of some samples from the stranded dataset between v12 and v13 * Response to @jharenza comments * Remove outdated output file * Update README for 07 * Use older version of annotated CNVkit file * Handled fusions consistent with #478 * Rerun with v13 data * Account for broad histology columns * Rerun whole pipeline * Use consensus CN files; rerun * Was using the CI files last time * Run copy number notebook with consensus calls * Fix filtering step HGG -> HGAT * Including the consensus CN calls was a little more nuanced * Rerun final notebook with upstream changes * Make sure notebook text is up to date * Update CN files in modules at a glance * Add other two K28M genes * Additional 2 genes in cleaned mutation * Response to @jharenza comments * Update documentation * Additional genes did not make it to documentation * Fix typo in subtype lable * Update analyses/molecular-subtyping-HGG/07-HGG-molecular-subtyping-combine-table.Rmd Co-Authored-By: Candace Savonen <cansav09@gmail.com> * Response to @cansavvy comments Co-authored-by: Candace Savonen <cansav09@gmail.com>
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Purpose/implementation Section
I am updating the
fusion-summarymodule to produce files that include all samples that are included in the original fusion files.What scientific question is your analysis addressing?
This is upstream of molecular subtyping of ependymoma tumors (#245) and non-MB, non-ATRT embryonal tumors (#251).
What was your approach?
In this pull request, I am changing the
fusion-summarymodule to generate files that include any sample that was included in either original fusion file (Arriba or STARFusion), rather than just those inpbta-fusion-putative-oncogenic.tsv. The rationale is that annotated fusions can be included in this file if they were detected by either caller - they are not required to be in both.See:
OpenPBTA-analysis/analyses/fusion_filtering/04-project-specific-filtering.Rmd
Line 242 in 8fba175
And the table mentioned in #92 (comment) contains the following note:
I'm adding this note explicitly to the
fusion_filteringREADME here because it tripped me up on #435.I also converted the fusion summary script (
01-fusion-summary.R) to a notebook (01-fusion-summary.Rmd) so I could better document some of the decision makingWhat GitHub issue does your pull request address?
Closes #477
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
The steps for generating the
fusion_summary*files, including theprepareOutputfunctionResults
What types of results are included (e.g., table, figure)?
Regenerated the following tables:
fusion_summary_embryonal_foi.tsvandfusion_summary_ependymoma_foi.tsv.Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.