Show detailed documentations of scMultiSim's parameters
Examples
scmultisim_help()
#> Call scmultisim_help(topic) where topic can be "options" or an option na
#> me. Printing help for options by default.
#> scMultiSim v1.0.0
#>
#> [GENERAL]
#>
#> rand.seed (default: 0)
#> scMultiSim should produce the same result if all other parameters are th
#> e same.
#> The value should be a numeric.
#> threads (default: 1)
#> Set to larger than 1 to use multithreading for some part of the simulati
#> on.
#> The value should be an integer between 1 and 4096.
#> speed.up (default: FALSE)
#> Use experimental speed and memory optimization.
#> The value should be a logical.
#>
#> [GENE]
#>
#> GRN (default: NULL)
#> The GRN network.
#> It should be a data frame with 3 columns (target, regulator, effect). Su
#> pply NA to disable the GRN effect.
#> grn.effect (default: 1)
#> Overall strength of the GRN effect on the expression. Different from the
#> effect column in the GRN data frame, which is the relative effect of ea
#> ch TF-target pair.
#> The value should be a numeric between 0 and Inf.
#> num.genes (default: NULL)
#> Number of genes if GRN is disabled.
#> The value should be an integer between 1 and Inf.
#> unregulated.gene.ratio (default: 0.1)
#> Ratio of unreulated to regulated genes. Extra unregulated genes will be
#> simulated in addition to the genes in GRN.
#> The value should be a numeric between 0 and 1.
#> giv.mean (default: 0)
#> Mean of the Gene Identity Vectors.
#> The value should be a numeric between -Inf and Inf.
#> giv.prob (default: 0.3)
#> Probability of non-zero values in the Gene Identity Vectors.
#> The value should be a numeric between 0 and 1.
#> giv.sd (default: 1)
#> Stddev of the Gene Identity Vectors.
#> The value should be a numeric between 0 and Inf.
#> hge.range (default: 1)
#> Only choose highly expressed genes after this range.
#> The value should be a numeric between 1 and Inf.
#> hge.prop (default: 0)
#> Propotion of highly expressed genes.
#> The value should be a numeric between 0 and 1.
#> hge.mean (default: 5)
#> Scale of highly expressed genes.
#> The value should be a numeric between 1 and Inf.
#> hge.sd (default: 1)
#> Variation of highly expressed genes.
#> The value should be a numeric between 0 and Inf.
#> hge.max.var (default: 500)
#> Genes with higher variation will not be selected as highly expressed gen
#> es.
#> The value should be a numeric between 0 and Inf.
#> dynamic.GRN (default: NA)
#> Specification of the dynamic GRN. See scmultisim_help("dynamic.GRN") for
#> details.
#>
#> [CELL]
#>
#> num.cells (default: 1000)
#> Total number of cells from all populations.
#> The value should be an integer between 0 and Inf.
#> tree (default: Phyla5())
#> A tree defining relationship between populations.
#> discrete.cif (default: FALSE)
#> Whether the cell population is discrete.
#> The value should be a logical.
#> discrete.pop.size (default: NA)
#> Specify the cell numbers in each population.
#> the value should be an integer vector
#> discrete.min.pop.size (default: 70)
#> Size of the smallest discrete cell population.
#> The value should be a numeric.
#> discrete.min.pop.index (default: 1)
#> Index of the smallest discrete cell population.
#> The value should be an integer between 0 and Inf.
#> num.cifs (default: 50)
#> Number of Cell Identity Factors for each kinetic parameter.
#> The value should be a numeric.
#> diff.cif.fraction (default: 0.9)
#> Fraction of CIFs which are differential factors between cell types.
#> The value should be a numeric between 0 and 1.
#> cif.center (default: 1)
#> Mean of the CIF values.
#> The value should be a numeric.
#> cif.sigma (default: 0.1)
#> Stddev of the CIF values.
#> The value should be a numeric between 0 and Inf.
#> use.impulse (default: FALSE)
#> Use the impulse model when generating the continuous CIF.
#> The value should be a logical.
#>
#> [SIMULATION - ATAC]
#>
#> atac.effect (default: 0.5)
#> The influence of chromatin accessability data on gene expression.
#> The value should be a numeric between 0 and 1.
#> region.distrib (default: c(0.1, 0.5, 0.4))
#> The probability that a gene is regulated by respectively 0, 1, 2 consecu
#> tive regions.
#> the value should be a vector with 3 elements sum to 1
#> atac.p_zero (default: 0.8)
#> The proportion of 0s we see in the ATAC-seq data.
#> atac.density (default: NA)
#> Density of the non-zero ATAC-seq values. Use atac_dens_nonzero() to gene
#> rate.
#> the value should be a density object.
#> riv.mean (default: 0)
#> Mean of the Region Identity Vectors.
#> The value should be a numeric between 0 and Inf.
#> riv.prob (default: 0.3)
#> Probability of non-zero values in the Region Identity Vectors.
#> The value should be a numeric between 0 and 1.
#> riv.sd (default: 1)
#> Stddev of the Region Identity Vectors.
#> The value should be a numeric between 0 and Inf.
#>
#> [SIMULATION - RNA]
#>
#> vary (default: s)
#> Which kinetic parameters have differential CIFs.
#> The value should be one of [all, kon, koff, s, except_kon, except_koff,
#> except_s].
#> bimod (default: 0)
#> Adjust the bimodality of gene expression, thus controlling intrinsic var
#> iation.
#> The value should be a numeric between 0 and 1.
#> scale.s (default: 1)
#> Scale of the s parameter. Use smaller value for cell types known to be s
#> mall (like naive cells). When discrete.cif = T, it can be a vector speci
#> fying the scale.s for each cluster.
#> intrinsic.noise (default: 1)
#> The weight assigned to the random sample from the Beta-Poisson distribut
#> ion, where the weight of the Beta-Poisson mean value is given a weight o
#> f (1 - intrinsic.noise).
#> The value should be a numeric between 0 and 1.
#>
#> [SIMULATION - KINETIC MODEL]
#>
#> do.velocity (default: FALSE)
#> Simulate using the whole kinetic model and generate RNA velocity data.
#> The value should be a logical.
#> beta (default: 0.4)
#> Splicing rate of each gene in the kinetic model.
#> The value should be a numeric.
#> d (default: 1)
#> Degradation rate of each gene in the kinetic model.
#> The value should be a numeric.
#> num.cycles (default: 3)
#> For velocity mode, the number of cycles run before sampling the gene exp
#> ression of a cell.
#> The value should be an integer between 1 and Inf.
#> cycle.len (default: 1)
#> For velocity mode, a factor multiplied by the expected time to transitio
#> n from kon to koff and back to form the the length of a cycle.
#> The value should be a numeric between 0 and Inf.
#> mod.cif.giv (default: NA)
#> Modify the generated CIF and GIV. The function takes four arguments: the
#> kinetic parameter index (1=kon, 2=koff, 3=s), the current CIF matrix, t
#> he GIV matrix, and the cell metadata dataframe. It should return a list
#> of two elements: the modified CIF matrix and the modified GIV matrix.
#> should be a function
#> ext.cif.giv (default: NA)
#> Add customized CIF and GIV. The function takes one argument, the kinetic
#> parameter index (1=kon, 2=koff, 3=s). It should return a list of two el
#> ements: the extra CIF matrix (n_extra_cif x n_cells) and the GIV matrix
#> (n_genes x n_extra_cif). Return NULL for no extra CIF and GIV.
#> should be a function
#>
#> [SIMULATION - SPATIAL]
#>
#> cci (default: NA)
#> The regulation network for spatial cell-cell interaction.
#> Enables cell-cell interaction. See scmultisim_help("cci") for details.
#> NULL