In ayurovsky/rnaGinesis: Simulate gene expression data

knitr::opts_chunk$set(echo = TRUE)

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Runs NMF on expression matrix from brain, liver, lung mixture data (GSE19830) saved in .RData, saves resultW and resultH to .NMF.result.RData

Loads .RData with list of simulated mixture data, trueH, trueW, unmixed data/signature matrices

load("~/rnaGinesis/data/Dataset_LiverLungBrain.RData")

Runs NMF on scRNA-seq mixture data and obtains resultW, resultH

# Calls helper method runNMF to run NMF on mixture
mixture <- Dataset_LiverLungBrain$ex
Dataset_LiverLungBrain.NMF <- runNMF(mixture = mixture, rank = 3)

Saves results from NMF to .RData file

save(Dataset_LiverLungBrain.NMF, file = "~/rnaGinesis/data/Dataset_LiverLungBrain.NMF.result.RData")

ayurovsky/rnaGinesis documentation built on Dec. 19, 2021, 6:36 a.m.