monarch-initiative / phenoCompare

Phenotype Compare

BSD 3-Clause "New" or "Revised" License

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Re-run analysis on new groupings #25

Open LCCarmody opened 4 years ago

LCCarmody commented 4 years ago

Could you re-run based on the 'New' groupings?

NEW groupings

Early2 (synthesis and transamidase)

DPM2 PIGY PIGA PIGC PIGH PIGP PIGQ PIGL PIGM PIGX PIGV PIGN PIGB PIGO PIGF PIGG PIGW DPM3 DPM1 MPDU1 PIGK GPAA1 PIGS PIGT PIGU

Late2 (modification)

PGAP1 PGAP3 PGAP2 PGAP5

@hannahblau @pnrobinson

OLD groupings

Early (synthesis)

DPM2 PIGY PIGA PIGC PIGH PIGP PIGQ PIGL PIGM PIGX PIGV PIGN PIGB PIGO PIGF PIGG PIGW DPM3 DPM1 MPDU1

Late (Transamidase and modification)

PIGT PIGK PIGS PIGU GPAA1

LCCarmody commented 4 years ago

Oops. I must have copied/pasted wrong: This is the old groupings which I took from here: https://github.com/monarch-initiative/phenoCompare/blob/master/src/main/resources/gpiGenesTwoGroups.txt

Early (synthesis)

DPM2 PIGY PIGA PIGC PIGH PIGP PIGQ PIGL PIGM PIGX PIGV PIGN PIGB PIGO PIGF PIGG PIGW DPM3 DPM1 MPDU1

Late (Transamidase and modification)

PIGT PIGK PIGS PIGU GPAA1 PGAP1 PGAP3 PGAP2 PGAP5

hannahblau commented 4 years ago

@LCCarmody @pnrobinson When I rerun my code using the new definitions of early and late genes, should I use the version of the HPO ontology that was current at the time of the original analysis in the paper, or do you want me to update my copy of hp.obo to the most recent release?

pnrobinson commented 4 years ago

Please use the same version!

hannahblau commented 4 years ago

You will find the new set of results in the directory named resultsRevised on the branch revisedGroups.

https://github.com/monarch-initiative/phenoCompare/tree/revisedGroups/resultsRevised

If you need something more, please ask. I wrote two R scripts as part of the phenoCompare project, not sure whether I need to re-run those. If this is all you need, please let me know so I can merge this branch into develop.