getPatientRankings {netDx} | R Documentation |
Process GM PRANK files to get the ROC curve for the query
getPatientRankings(pFile, pheno_DF, predClass, plotIt = FALSE, verbose = FALSE)
pFile |
(char) path to PRANK file |
pheno_DF |
(data.frame) patient IDs ('ID') and label('STATUS') |
predClass |
(character) class label for which predictor is built |
plotIt |
(logical) if TRUE plots ROC curve |
verbose |
(logical) print messages |
(list) 1) predLbl: GeneMANIA scores (predicted labels). Higher score for higher ranked patient. 2) realLbl: binary value indicating if patient label matches predictor label (real labels) 3) fullmat: pheno_DF merged with similarity scores ('similarityScore') and real label ('isPredClass') 4) roc: output of ROCRs performance(,'tpr','fpr') - ROC curve 5) auc: output of ROCRs auc() 6) precall: output of ROCRs performance(, 'prec','rec') 7) f: output of ROCRs performance(,'f') If < 2 patients in PRANK file, roc,auc, precall, f are all returned as NA.
data(pheno) prankFile <- system.file("extdata", paste("GM_PRANK","CV_1.query-results.report.txt.PRANK",sep=getFileSep()), package="netDx") x <- getPatientRankings(prankFile, pheno, 'LumA')