getPatientRankings {netDx} | R Documentation

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

### Description

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

### Usage

    getPatientRankings(pFile, pheno_DF, predClass, plotIt = FALSE,
      verbose = FALSE)

### Arguments

`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

### Value

(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.

### Examples

    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')

[Package netDx version 1.0.3 Index]