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removing rownames from reference files #836
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jharenza
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Nov 9, 2020
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@kgaonkar6 thanks for this - will it break anything in fusion-filtering right now?
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It doesn't break the script, it's only used https://github.com/kgaonkar6/OpenPBTA-analysis/blob/23a116afbd2da387fbc1e59143df3549aa94460c/analyses/fusion_filtering/02-fusion-filtering.R#L241-L255 which works fine now as well |
jharenza
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Nov 9, 2020
for annot file, update read.delim2 to read_tsv since [AlexsLemonade#836](AlexsLemonade#836) has gone in
jaclyn-taroni
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Nov 12, 2020
* add fusion summary for LGAT * fix subsetFuseLGAT fix variable name subsetFuseLGAT * add comments from code review add comments from @cansavvy and @kgaonkar6 code review * consolidate function consolidate filterFusion() and filterLGATFusion() functions * tidy final rbind step - select only BS_ID and fusion - add distinct * clarify code update code from @cansavvy code review * update read.delim2 to read_tsv for annot file, update read.delim2 to read_tsv since [#836](#836) has gone in * Try moving fusion summary up Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
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Purpose/implementation Section
What scientific question is your analysis addressing?
Updating format for input gene and fusion list to be compatible with read_tsv and updating README
What was your approach?
I saved the file with write_tsv() so now the files can be read with read.delim as well as read_tsv()
What GitHub issue does your pull request address?
#832
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
I'm linking to the code I'd used originally to format the and create the file does that sound ok?
Is there anything that you want to discuss further?
NA
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
NA
Results
What types of results are included (e.g., table, figure)?
NA
What is your summary of the results?
NA
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.