In ayurovsky/rnaGinesis: Simulate gene expression data

knitr::opts_chunk$set(echo = TRUE)

R Markdown

Runs NMF on expression matrix from scRNA-seq mixture data 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_ResampledSingleCell.RData")

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

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

Saves results from NMF to .RData file

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

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