getEMapInput: write enrichment map for consensus nets
In BaderLab/netDx: Network-based patient classifier

Description Usage Arguments Value Examples

write enrichment map for consensus nets

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

`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

(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).

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("October",2020))
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)