estimate.expression: estimate.expression

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

Description

Estimate the expected expression levels for entries in the gene by cell expression matrix

Usage

estimate.expression(X, ks = 10:15, dists = c("spearman", "pearson"),
  dim.reduc.prop = 0.05, max.dim = 100, pc.cdr.cc.cutoff = 1,
  mc.cores = 1, batch.size = NA)

Arguments

X	Log transformed gene expression matrix (Gene by Cell).
ks	Number of cell clustering groups. (default: 10:15)
dists	Distribution matrices to use. (default: c("spearman", "pearson"))
dim.reduc.prop	Proportion of principal components to use for K-means clustering. (default: 0.05)
max.dim	Maximum dimensions for PCA (default: 100)
pc.cdr.cc.cutoff	The PC's which correlation coefficient with CDR (cellular detection rate) will be removed. (default: 1)
mc.cores	Number of CPU cores (default: 1)
batch.size	Batch size of sampling based MDS approximation

Value

A matrix object

Author(s)

Wuming Gong

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

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