ruvSimulate {scMerge}R Documentation

Simulate a simple matrix or SingleCellExperiment to test internals of scMerge

Description

This function is designed to generate Poisson-random-variable data matrix to test on the internal algorithms of scMerge. It does not represent real biological situations and it is not intended to be used by end-users.

Usage

ruvSimulate(m = 100, n = 5000, nc = floor(n/2), nCelltypes = 3,
  nBatch = 2, k = 20, lambda = 0.1, sce = FALSE)

Arguments

m

Number of observations

n

Number of features

nc

Number of negative controls

nCelltypes

Number of cell-types

nBatch

Number of batches

k

Number of unwanted factors in simulation

lambda

Rate parameter for random Poisson generation

sce

If TRUE, returns a SingleCellExperiment object

Value

If sce is FALSE, then the output is a list consists of

if sce is TRUE, a SingleCellExperiment wrapper will be applied on all above simulated objects.

Examples

set.seed(1)
L = ruvSimulate(m = 200, n = 1000, nc = 200, 
nCelltypes = 3, nBatch = 2, lambda = 0.1, k = 10, sce = TRUE)
print(L)
example <- scMerge(sce_combine = L,
                      ctl = paste0('gene', 1:500),
                      cell_type = L$cellTypes,
                      ruvK = 10,
                      assay_name = 'scMerge')
                      
scater::plotPCA(L, colour_by = 'cellTypes', shape = 'batch',
                 run_args = list(exprs_values = 'logcounts'))
                 
scater::plotPCA(example, colour_by = 'cellTypes', shape = 'batch',
                 run_args = list(exprs_values = 'scMerge'))

[Package scMerge version 1.2.0 Index]