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LieberInstitute / zandiHyde_bipolar_rnaseq

RNA-seq analysis for psychENCODE R01
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Export TWAS results to a table #5

Closed lcolladotor closed 3 years ago

lcolladotor commented 3 years ago

Hi Arta,

Once #2 is done, we need to create a table with the TWAS significant results across all 4 feature types (gene, exon, exon-exon junction, transcript). We also need to save the TWAS sACC vs Amygdala results. This involves adapting the code from https://github.com/LieberInstitute/brainseq_phase2/blob/master/supp_tabs/twas_supp.R#L1-L40.

Best, Leo

aseyedia commented 3 years ago

TWAS significant results across all 4 feature types (gene, exon, exon-exon junction, transcript)

I'm a bit confused, because I thought we only produced TWAS results for genes? Generating significant TWAS results across the other 3 feature types you mentioned would require me to go back to filter_snps.R to modify the code, and potentially adapting the rest of the pipeline to include the other feature types as well. I'm happy to do this, I just wanted to make sure this is what you meant.

lcolladotor commented 3 years ago

Just genes. I made a mistake when I first wrote that issue. I think that you've done this already and shared with Peter, so we can close this.

lcolladotor commented 3 years ago

Sorry, I think that it's best if you confirm that this is done and close the issue yourself. Thanks!

aseyedia commented 3 years ago

I've exported them as separate CSVs but haven't yet used the xslx package to export them as all the same file with tables on different sheets. This would be a trivial task and I could do this in a manner of minutes.

lcolladotor commented 3 years ago

I guess that you've never installed rJava hehe ;)

But yeah, sounds like you are nearly done with this project then. So we can resume the NAc one then.

aseyedia commented 3 years ago

Here is the final output table with all of the attached sheets: /dcl01/lieber/ajaffe/lab/zandiHyde_bipolar_rnaseq/dev_twas/analysis/tables/BD_Amyg_sACC_FinalOutputTable.xlsx