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.
1 2 3 |
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 |
drop.method |
Dropout method, with two options: zero-inflation (default), or low-rate Poisson. Will only be used if |
drop.lambda |
Mean of low-rate Poisson for the Poisson-dropout scenario. Will only be used if |
DGElist object containing all simulation settings and results, including the count matrix and dropout-imposed count matrix.
1 2 3 4 | # 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
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