##
## predict from one dataset to another
##
library(fendR)
library(synapseClient)
library(dplyr)
all.datasets=c('CCLE','Sanger','NTAP')
#build fendR from dataset
buildFendRFromDataset<-function(ds.name,use.rna=TRUE,responseNorm=NA,geneNorm=NA){
if(!ds.name%in%all.datasets){
print(paste(ds.name,'not available, select from:',paste(all.datasets,collapse=',')))
return(NULL)
}
network.file<-'https://github.com/fraenkel-lab/OmicsIntegrator/raw/master/data/iref_mitab_miscore_2013_08_12_interactome.txt'
if(ds.name=='Sanger'){
gene.file<-system.file('SANGER_binaryEventMatrix.tsv',package='fendR')
gene.data<-loadSampleData(gene.file)
rna.seq.data<-system.file('SANGER_brainarray_rma_expr.tsv.gz', package='fendR')
rna.data<-loadSampleData(rna.seq.data)
pheno.file<-system.file('SANGER_dose_response_AUC.tsv',package='fendR')
pheno.data<-loadPhenotypeData(pheno.file)
target.file<-system.file('SANGER_drugGeneTargets.tsv',package='fendR')
target.data<-loadTargetData(target.file)
}else if(ds.name=='CCLE'){
gene.file<-system.file('CCLE_binary_mutation_matrix_ucscGenesFromCBioPortal.tsv',package='fendR')
gene.data<-loadSampleData(gene.file)
rna.seq.data<-system.file('CCLE_medianZscore_rnaSeq_ucscGenesFromCbioPortal.tsv.gz', package='fendR')
rna.data<-loadSampleData(rna.seq.data)
pheno.file<-system.file('CTRP_v20_AUC_vales_by_drug.tsv',package='fendR')
pheno.data<-loadPhenotypeData(pheno.file)
target.file<-system.file('CTRP_v20_drug_target_vals.tsv',package='fendR')
target.data<-loadTargetData(target.file)
}else if(ds.name=='NTAP'){
require(synapseClient)
synapseLogin()
gene.data<-read.table(synGet('syn8304629')@filePath,header=T)
#gene.data<-loadSampleData(gene.file)
# rna.seq.data<-
rna.data<-read.table(synGet('syn8304627')@filePath,header=T)
pheno.data<-read.table(synGet('syn8304620')@filePath,header=T)
pheno.data<-pheno.data[-which(is.na(pheno.data$Phenotype)),]
# pheno.data<-loadPhenotypeData(pheno.file)
target.data<-read.table(synGet('syn8304095')@filePath,header=T)
target.data<-target.data[-which(is.na(target.data$Gene)),]
}
if(use.rna)
gene.data <- rna.data
target.genes<-unique(target.data$Gene)
fObj <- basicFendR(networkFile=network.file,
featureData=gene.data,
sampleOutcomeData=pheno.data,
phenoFeatureData = target.data,
targetGenes=target.genes,
responseNorm=responseNorm,
geneNorm=geneNorm
)
return(fObj)
}
#add in quick zscore function
zscore <-function(x){
(x-mean(x,na.rm=T))/sd(x,na.rm=T)
}
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