getFeatureScores: Compile network scores into a matrix

Description Usage Arguments Details Value Examples

View source: R/getFeatureScores.R

Description

Compile network scores into a matrix

Usage

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getFeatureScores(inDir, predClasses, getFullCons = TRUE)

Arguments

inDir

(char/list) directory containing directories with all split info or list of all CV score files. if inDir is a single directory then the expected format for CV score files is <inDir>/rngX/predClassX/GM_results/predClassX_pathway_CV_score.txt' if inDir is a list, it should have one key per class. The value should be the corresponding set of filenames for pathway_CV_score.txt

predClasses

(char) possible STATUS for patients

getFullCons

(logical) if TRUE, does not remove rows with NA. Recommended only when the number of input features is extensively pruned by first-pass feature selection.

Details

Given network scores over a set of train/test splits, compiles these into a matrix for downstream analysis. See the section on 'Output Files'

Value

(list) one key per patient class. Value is matrix of network scores across all train/test splits. Each score is the output of the inner fold of CV.

Examples

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inDir <- system.file("extdata","example_output",package="netDx")
netScores <- getFeatureScores(inDir, predClasses = c('LumA','notLumA'))

netDx documentation built on Dec. 11, 2020, 2:01 a.m.