scRMD: Imputation for single cell RNA-seq data via restricted robust matrix decomposition

Chong Chen, Changjing Wu 2017-9-14

Introduction

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.

Installation

scRMD can be installed by simplely run:

install.packages("devtools")         
library(devtools)           
install_github("XiDsLab/scRMD")

Quick start

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(sData$de[sData$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)