getEMapInput {netDx} | R Documentation

## write enrichment map for consensus nets

### Description

write enrichment map for consensus nets

### Usage

    getEMapInput(featScores, namedSets, netInfo, pctPass = 0.7,
      minScore = 1, maxScore = 10, trimFromName = c(".profile", "_cont"),
      verbose = FALSE)

### Arguments

`featScores` | (data.frame) network scores across rounds of cross validation. Rows are networks and columns are network name followed by scores for cross-validation rounds. Output of getFeatureScores()
`namedSets` | (list) list of nets and units (e.g.e pathway names and genes). Should only contain units profiled in this dataset
`netInfo` | (data.frame) Table of network name (netName) and type (netType). Type is used to assign shapes to nodes: clinical clinical rna GUANOSINE_NUCLEOTIDES__I_DE_NOVO__I__BIOSYNTHESIS rna RETINOL_BIOSYNTHESIS
`pctPass` | (numeric between 0 and 1) fraction of splits for which the highest score for the network is required, for that to be the network's maxScore
`minScore` | (integer) features with score below this cutoff are excluded from downstream analyses
`maxScore` | (integer) maximum possible score in one round of cross- validation. e.g. for 10-fold cross-validation, maxScore=10.
`trimFromName` | (char) strings to trim from name with sub()
`verbose` | (logical) print messages

### Value

(list) Length two. 1) nodeAttrs: data.frame of node attributes 2) featureSets: key-value pairs of selected feature sets (e.g. if pathway features are used, keys are pathway names, and values are member genes).

### Examples

    inDir <- system.file("extdata","example_output",package="netDx")
    outDir <- paste(tempdir(),'plots',sep='/')
    if (!file.exists(outDir)) dir.create(outDir)
    featScores <- getFeatureScores(inDir,predClasses=c('LumA','notLumA'))
    gp <- names(featScores)[1]
    pathwayList <- readPathways(fetchPathwayDefinitions())
    pathwayList <- pathwayList[seq_len(5)]
    netInfoFile <- system.file("extdata","example_output/inputNets.txt",package="netDx")
    netInfo <- read.delim(netInfoFile,sep='\t',h=FALSE,as.is=TRUE)
    emap_input <- getEMapInput(featScores[[gp]],pathwayList,netInfo)
    summary(emap_input)

[Package netDx version 1.0.3 Index]