simulateDropoutCounts: Generate simulation data from negative binomial (NB)...

In rikenbit/fuchikoma: Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data

Description

This function generates simulation data with arbitrary defined experimental condition.

Usage

simulateDropoutCounts(Ngene = 10000, makeDEG=TRUE, PDEG = 0.02, DEG.assign = c(0.5, 0.5), DEG.thr = c("E1", "E1"), replicates = c(48, 48), Lambda = 1)

Arguments

Ngene	No. of gene (defalult:10000)
makeDEG	Whether make DEG or not (defalult:TRUE)
PDEG	Percentage of DEG (defalult:0.02)
DEG.assign	Ratio of DEG in each cluster (defalult:c(0.5, 0.5))
DEG.thr	Fold change in each cluster (defalult:c("E5", "E5"))
replicates	No of repeated measurement in each cluster (defalult:c(3, 3))
Lambda	(defalult:0.1)

Value

DEG	DEG list
FC	Design matrix specifying fold change
Simcount	Count data.frame generated by this function

Author(s)

Koki Tsuyuzaki, Haruka Ozaki, Mika Yoshimura, Itoshi Nikaido

Maintainer: Koki Tsuyuzaki <[e-mail]>

Examples

res1 <- simulateDropoutCounts()
str(res1)

rikenbit/fuchikoma documentation built on May 27, 2019, 9:09 a.m.