DrImpute: DrImpute

In gongx030/DrImpute: Imputing Dropout Events in Single-Cell RNA-Sequencing Data

Description

Imputing dropout events in single-cell RNA-sequencing data.

Usage

DrImpute(X, ks = 10:15, dists = c("spearman", "pearson"),
  batch.size = NA, mc.cores = 1)

Arguments

X	Gene expression matrix (gene by cell).
ks	Number of cell clustering groups. Default set to ks = 10:15.
dists	Distribution matrices to use. Default is set to c("spearman", "pearson"). "eucleadian" can be added as well.
batch.size	Batch size of sampling based MDS approximation; if batch.size is NA, the standard MDS is used.
mc.cores	Number of CPU cores (default: 1)

Value

A matrix object

Author(s)

Wuming Gong and Il-Youp Kwak

References

Wuming Gong, Il-Youp Kwak, Pruthvi Pota, Kaoko Koyano-Nakagawa and Daniel J. Garry (2017+) DrImpute: Imputing dropout eveents in single cell RNA sequencing data

Examples

library(scDatasets)
library(SummarizedExperiment)
data(usoskin)
X <- assays(usoskin)$count
X <- preprocess(X, min.expressed.gene = 0)
X.log <- log(X + 1)
set.seed(1)
X.imp <- DrImpute(X.log)

gongx030/DrImpute documentation built on Dec. 10, 2020, 6:23 p.m.