Update machinelearning-functions-PerTurbo.R

[mgerault]

Hello,

I don't know if it's because of the new R version but call max with i like this only return one value; as a consequence all prediction scores from perTurbo are the same for each protein with unknown location. Calling max with apply prevent from this issue.
I didn't check but it's maybe the case with other machine learning functions from pRoloc.

[lgatto]

Thank you @mgerault - would have have some small test data for us to reproduce this and possibly add a unit test.

@samWieczorek, could you also look at this (as well as #147) , given that, as far as I can remember, you originally contributed that code.

[mgerault]

@lgatto I tested it with tan2009r1 dataset from pRolocdata package and other like dunkley2006 etc.
Also, I compared with knn and svm, the results are totally different from perTurbo algorithm --> checked with plot2D and in fData predictions results.

[lgatto]

Thank you very much - I'll look at it asap.

[lgatto]

@samWieczorek - no comment about this?

[lgatto]

Thank you @mgerault - this PR certainly makes sens. I would probably favour

rowMax(ans[i, ])

for clarity and not dropping the i sub-setting from the original code.

@samWieczorek - I will be waiting for your input in this PR and especially #147 before merging.

[lgatto]

Thank you @mgerault, I'll merge now and push to Bioc. But I haven't hear from @samWieczorek, and might consider deprecating the PerTurbo functions in the future, unless you use them.

[mgerault]

Hi lgatto, Honestly It's one of the best algorithm with TAGM so it would be a shame to remove it. Kind regards Mgerault Le mer. 21 sept. 2022, 21:00, Laurent Gatto ***@***.***> a écrit :

…

Thank you @mgerault <https://github.com/mgerault>, I'll merge now and push to Bioc. But I haven't hear from @samWieczorek <https://github.com/samWieczorek>, and might consider deprecating the PerTurbo functions in the future, unless you use them. — Reply to this email directly, view it on GitHub <#146 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQENY3Z3RXVWILUQDEQXJBLV7NLMLANCNFSM5YTKHXEA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[lgatto]

OK then, thank you for letting me know. Will keep it. Thanks again for fixing the bug!