Chong Chen, Changjing Wu 2017-9-14
scRMD is developed to impute single cell RNA data with dropouts. scRMD assumes the the underlying expression profile of genes is low rank and the dropout events are rare compared with true zero expression.
scRMD can be installed by simplely run:
install.packages("devtools")
library(devtools)
install_github("ChongC1990/scRMD")library(scRMD)
set.seed(2017)
K=3; Kn=50; Ndiff=100; Nsame=10000; logMean=1.8; logSd=0.5;
ZeroRate = 0.5; sigmahetero = 0.1; sigmahomo = 0.2; drbase = 1; dr = 0.2;
sData = sSimulator(K, Kn, Ndiff, Nsame, logMean, logSd, ZeroRate, drbase, dr, sigmahomo, sigmahetero, type = "cluster")
cutoff = quantile(sDate$de[sDate$de>0], 0.05)
res.rmd <- rmd(sData$de, candidate = cutoff)
pca.rmd <- prcomp(res.rmd$exprs)
cl.rmd <- kmeans(pca.rmd$x[,1:2],K,nstart = 100)
CalculateARI(sData$label, cl.rmd$cluster)