search

papaemmelab / ipssm

Molecular International Prognostic Scoring System IPSS-M for Myelodysplastic Syndromes
Other
8 stars 5 forks source link

How to calculate IPSS-R score? #7

Closed SixPlusSeven closed 3 months ago

SixPlusSeven commented 1 year ago

Hello,

Could you tell me how to calculate IPSS-R score and IPSS-R score (age-adjusted) using ipssm package? I can see these two values on the web version, but I can't calculate them using the R package locally. In addition, I added two columns "ANC" and "AGE" to the IPSSMexample.csv file for local calculation. ID,HB,PLT,BM_BLAST,ANC,AGE,del5q,del7_7q,complex,CYTO_IPSSR,del17_17p,TP53mut,TP53maxvaf,TP53loh,MLL_PTD,FLT3,ASXL1,BCOR,BCORL1,CBL,CEBPA,DNMT3A,ETV6,EZH2,IDH1,IDH2,KRAS,NF1,NPM1,NRAS,RUNX1,SETBP1,SF3B1,SRSF2,STAG2,U2AF1,ETNK1,GATA2,GNB1,PHF6,PPM1D,PRPF8,PTPN11,WT1 pp347,9.6,281,9,3,19,0,0,0,Good,0,0,NA,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,NA,0,NA,0,0,NA,0,0

Best, Alex

ElsaB commented 1 year ago

Hello

You are correct, in the R package we did not implement the IPSS-R calculation, only the IPSS-M. We added the IPSS-R in the web for the clinicians to have all in the information in one place. For statisticians/analysts using R, IPSS-R is vey easy to calculate using the sum of the points attributed to the categories of features (as explained in https://www.mds-foundation.org/ipss-r-calculator/ ).

Best Elsa

SixPlusSeven commented 1 year ago

Thank you for your answer.

Can I calculate the IPSS-R by myself? Do I need to build my own fitting function based on the distribution of points? Where can I get the data for these points?

Best, Alex

m6oland commented 1 year ago

You can use the clinical data to calculate IPSS-R. The algorithm is pretty simple as is the age adjustment. IPSSRannotate.txt