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umccr / RNAsum

Pipeline for generating RNAseq-based cancer patient reports
https://umccr.github.io/RNAsum/
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Rmd refactor4 pd #84

Closed pdiakumis closed 1 year ago

pdiakumis commented 1 year ago

@skanwal sorry for delay, I've done the refactor of the gene summaries as discussed. I think there was a bug in master at https://github.com/umccr/RNAsum/blob/e1dc8ebe1dea0f7ea310eb5337340edcfb0110c6/rmd_files/RNAseq_report.Rmd#L2407 (instead of 'Mutated', that should be 'Fusion'). Ignore the auto-generated man/ files, main changes are in the Rmd and R/sample_data.R.

skanwal commented 1 year ago

Thanks @pdiakumis.

I think there was a bug in master

You're right. I had picked it up during refactor work and corrected it here https://github.com/umccr/RNAsum/blob/rmd_refactor4/inst/rmd/rnasum.Rmd#L472 in my refactor branch.

skanwal commented 1 year ago

I have tested this PR and the changes work nicely. I am thinking we can go through these quickly tomorrow in our 1-1 and then merge it in rmd_refactor4 branch.

pdiakumis commented 1 year ago

@skanwal I refactored a couple more chunks, nothing too fancy. I've also added some lib size barplot questions we can talk about next week.