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#' Run PAC for Specified Samples
#'
#' A wrapper to run PAC and output subpopulation mutual information networks. Please use the PAC function itself for individual samples or if the MAN step is not needed.
#'
#'
#' @param sampleIDs sampleID vector
#' @param dim_subset a string vector of string names to subset the data columns for PAC; set to NULL to use all columns
#' @param hyperrectangles number of hyperrectangles to learn for each sample
#' @param num_PACSupop number of subpopulations to output for each sample using PAC
#' @param max.iter postprocessing kmeans iterations
#' @param num_networkEdge a threshold on the number of edges to output for each subpopulation mutual information network
#' @export
#' @examples
#' Please see vignette for the PAC-MAN tutorial
samplePass<-function(sampleIDs, dim_subset, hyperrectangles,num_PACSupop, max.iter,num_networkEdge){
for(i in 1:length(sampleIDs)){
load(paste0(sampleIDs[i], ".Rdata"))
inputMatrix<-get(sampleIDs[i])
#subset for dimensions involved in clustering of subpopulations
if(!is.null(dim_subset)){
inputMatrix_dimsubset<-inputMatrix[,dim_subset]
subpopulationLabels = PAC(inputMatrix_dimsubset, num_PACSupop, maxlevel = hyperrectangles, method = "dsp", max.iter = max.iter)
save(subpopulationLabels, file=paste0(sampleIDs[i], "_subpopulationLabels.Rdata"))
inputMatrix_withSampleName<-cbind(sampleIDs[i], as.data.frame(inputMatrix))
data_agg<-aggregateData(inputMatrix_withSampleName,subpopulationLabels)
save(data_agg, file=paste0(sampleIDs[i], "_data_agg.Rdata"))
save(inputMatrix_withSampleName, file=paste0(sampleIDs[i], "_dataMatrix.Rdata"))
mainDir <- getwd()
subDir <- paste0("/", sampleIDs[i], "_SampleSubpopulationMatrixNetworks")
dir.create(file.path(mainDir, subDir))
setwd(paste0(mainDir, subDir))
inputMatrix_dimsubset_withSampleName<-cbind(sampleIDs[i], as.data.frame(inputMatrix_dimsubset))
outputNetworks_topEdges_matrix(inputMatrix_dimsubset_withSampleName, subpopulationLabels, threshold=(2*num_networkEdge))
setwd(mainDir)
}else{
subpopulationLabels = PAC(inputMatrix, num_PACSupop, maxlevel = hyperrectangles, method = "dsp", max.iter = max.iter)
save(subpopulationLabels, file=paste0(sampleIDs[i], "_subpopulationLabels.Rdata"))
inputMatrix_withSampleName<-cbind(sampleIDs[i], as.data.frame(inputMatrix))
data_agg<-aggregateData(inputMatrix_withSampleName,subpopulationLabels)
save(data_agg, file=paste0(sampleIDs[i], "_data_agg.Rdata"))
save(inputMatrix_withSampleName, file=paste0(sampleIDs[i], "_dataMatrix.Rdata"))
mainDir <- getwd()
subDir <- paste0("/", sampleIDs[i], "_SampleSubpopulationMatrixNetworks")
dir.create(file.path(mainDir, subDir))
setwd(paste0(mainDir, subDir))
outputNetworks_topEdges_matrix(inputMatrix_withSampleName, subpopulationLabels, threshold=(2*num_networkEdge))
setwd(mainDir)
}
}
}
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