Rank-Scoring for predictions

[b-schubert]

Transformation of prediction score to its rank based on empirically approximated scoring distribution using random peptides of natural proteins

[monikasekelja]

Hi,

Thank you for the great software! Regarding the rank values - is there a simple way of changing the code to obtain the rank values in stead of affinity scores from NetMHCpan and NetMHCIIpan? I see that both programs write the rank values in the output result file...

[b-schubert]

Hi @monikasekelja

Thanks!

Regarding the rank scores:

Each of the external prediction methods under Fred2.EpitopePrediction.External implement a method called parse_external_resultwhich reads usually the excel output of NetMHC. It should be fairly simple to adjust the code so that it returns the rank scores by just shifting the hard coded index of the IC50-values to the rank-scores.

If you need help, let me know.

[monikasekelja]

I changed the ic_pos to 6 and it worked! Thanks!