getPatientRankings: Process GM PRANK files to get the ROC curve for the query
In netDx: Network-based patient classifier

Description Usage Arguments Value Examples

Process GM PRANK files to get the ROC curve for the query

1	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')