sim.scRNAseq: Simulating scRNA-seq expression data
In fayezor/myRpackage:

Description Usage Arguments Value Examples

Extract parameters from real dataset to simulate scRNA-seq expression data with differentially expressed genes; options for imposing dropouts on the data.

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sim.scRNAseq(dataset, nlibs = NULL, nTags = NULL, design = NULL,
  beta = NULL, drop.low.lambda = TRUE, drop.extreme.dispersion = 0.1,
  lib.size = NULL, flibs = c(0.7, 1.3), verbose = TRUE, seed = NULL)

`dataset`	Numeric matrix of read counts from which to extract parameters.
`nlibs`	Desired number of replicates per group.
`nTags`	Desired number of genes. If not provided, simulated dataset will contain as many genes as the real dataset.
`design`	Model matrix (without an intercept) that you would like to simulate from
`beta`	Set of coefficients for the model matrix (must have same number of columns as mod)
`drop.low.lambda`	Logical, whether to drop low lambdas.
`drop.extreme.dispersion`	Proportion of extreme dispersions to drop.
`lib.size`	Numeric vector giving the total count (sequence depth) for each library. If not provided, library sizes are extracted from the real dataset.
`flibs`	Some wiggle room for the library sizes extracted from real dataset.
`verbose`	Logical, whether to print simulation progress to screen.
`seed`	Optional seed, if it desired to replicate the simulation.
`add.dropout`	Logical, whether to impose dropouts.
`pDropout`	Numeric vector of dropout probabilities to consider. Will only be used if `add.dropout=TRUE`.
`drop.method`	Dropout method, with two options: zero-inflation (default), or low-rate Poisson. Will only be used if `add.dropout=TRUE`.
`drop.lambda`	Mean of low-rate Poisson for the Poisson-dropout scenario. Will only be used if `add.dropout=TRUE` and `drop.method="poisson"`.

DGElist object containing all simulation settings and results, including the count matrix and dropout-imposed count matrix.

# Simulate toy dataset with 3 reps per group and 20 genes
# data(prostatedata)
#simData <- sim.scRNAseq(dataset=prostatedata, nreps=3, nTags=20, drop.method=c("zero"))
NULL

fayezor/myRpackage documentation built on May 16, 2019, 11:01 a.m.