createPSN_MultiData: Wrapper to create custom input features (patient similarity...

In BaderLab/netDx: Network-based patient classifier

Description

Wrapper to create custom input features (patient similarity networks)

Usage

createPSN_MultiData(
  dataList,
  groupList,
  pheno,
  netDir = tempdir(),
  filterSet = NULL,
  verbose = TRUE,
  customFunc,
  ...
)

Arguments

dataList	(list) key is datatype (e.g. clinical, rna, etc.,), value is table or RangedData) Note that unit names should be rownames of the data structure. e.g If dataList$rna contains genes, rownames(dataList) = gene names
groupList	(list) key is datatype; value is a list of unit groupings for that datatype. e.g. If rna data will be grouped by pathways, then groupList$rna would have pathway names as keys, and member genes as units. Each entry will be converted into a PSN.
pheno	(data.frame) mapping of user-provided patient identifiers (ID) with internally-generated identifiers.
netDir	(char) path to directory where networks will be stored
filterSet	(char) vector of networks to include
verbose	(logical) print messages
customFunc	(function) custom user-function to create PSN. Must take dataList,groupList,netDir as parameters. Must check if a given groupList is empty (no networks to create) before the makePSN call for it. This is to avoid trying to make nets for datatypes that did not pass feature selection
...	other parameters to makePSN_NamedMatrix() or makePSN_RangedSets()

Value

(char) vector of network names. Side effect of creating the nets

Examples

library(curatedTCGAData)
library(MultiAssayExperiment)
curatedTCGAData(diseaseCode='BRCA', assays='*',dry.run=TRUE,version="1.1.38")

# fetch mrna, mutation data
brca <- curatedTCGAData('BRCA',c('mRNAArray'),FALSE,version="1.1.38")

# get subtype info
pID <- colData(brca)$patientID
pam50 <- colData(brca)$PAM50.mRNA
staget <- colData(brca)$pathology_T_stage
st2 <- rep(NA,length(staget))
st2[which(staget %in% c('t1','t1a','t1b','t1c'))] <- 1
st2[which(staget %in% c('t2','t2a','t2b'))] <- 2
st2[which(staget %in% c('t3','t3a'))] <- 3
st2[which(staget %in% c('t4','t4b','t4d'))] <- 4
pam50[which(!pam50 %in% 'Luminal A')] <- 'notLumA'                         
pam50[which(pam50 %in% 'Luminal A')] <- 'LumA'
colData(brca)$ID <- pID
colData(brca)$STAGE <- st2                                                 
colData(brca)$STATUS <- pam50

# keep only tumour samples
idx <- union(which(pam50 == 'Normal-like'), which(is.na(st2)))
cat(sprintf('excluding %i samples\n', length(idx)))
                                                                           
tokeep <- setdiff(pID, pID[idx])
brca <- brca[,tokeep,]

pathList <- readPathways(fetchPathwayDefinitions("October",2020))

brca <- brca[,,1] # keep only clinical and mRNA data

# remove duplicate arrays
smp <- sampleMap(brca)
samps <- smp[which(smp$assay=='BRCA_mRNAArray-20160128'),]
notdup <- samps[which(!duplicated(samps$primary)),'colname']
brca[[1]] <- brca[[1]][,notdup]

groupList <- list()
groupList[['BRCA_mRNAArray-20160128']] <- pathList[seq_len(3)]
makeNets <- function(dataList, groupList, netDir,...) {
    netList <- c()
    # make RNA nets: group by pathway
    if (!is.null(groupList[['BRCA_mRNAArray-20160128']])) {
    netList <- makePSN_NamedMatrix(dataList[['BRCA_mRNAArray-20160128']],
                rownames(dataList[['BRCA_mRNAArray-20160128']]),
                groupList[['BRCA_mRNAArray-20160128']],
                netDir,verbose=FALSE,
                writeProfiles=TRUE,...)
    netList <- unlist(netList)
    cat(sprintf('Made %i RNA pathway nets\n', length(netList)))
    }

    cat(sprintf('Total of %i nets\n', length(netList)))
    return(netList)
}

exprs <- experiments(brca)
datList2 <- list()
for (k in seq_len(length(exprs))) {
 tmp <- exprs[[k]]
 df <- sampleMap(brca)[which(sampleMap(brca)$assay==names(exprs)[k]),]
 colnames(tmp) <- df$primary[match(df$colname,colnames(tmp))]
 tmp <- as.matrix(assays(tmp)[[1]]) # convert to matrix
 datList2[[names(exprs)[k]]]<- tmp
}
pheno <- colData(brca)[,c('ID','STATUS')]
netDir <- tempdir()
pheno_id <- setupFeatureDB(colData(brca),netDir)
createPSN_MultiData(dataList=datList2,groupList=groupList,
 pheno=pheno_id,
 netDir=netDir,customFunc=makeNets,numCores=1)

BaderLab/netDx documentation built on Sept. 26, 2021, 9:13 a.m.