getEMapInput: write enrichment map for consensus nets

Description Usage Arguments Value Examples

View source: R/getEmapInput.R

Description

write enrichment map for consensus nets

Usage

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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

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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)

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