True2ObservedCounts: Simulate observed count matrix given technical biases and the...

In Galaxeee/TedSim: Temporal Dynamics Simulation of scRNA-seq and CRISR/Cas9 lineage barcodes

Simulate observed count matrix given technical biases and the true counts

Description

Simulate observed count matrix given technical biases and the true counts

Usage

True2ObservedCounts(
  SE = NULL,
  true_counts,
  meta_cell,
  protocol,
  alpha_mean = 0.1,
  alpha_sd = 0.002,
  lenslope = 0.02,
  nbins = 20,
  gene_len,
  amp_bias_limit = c(-0.2, 0.2),
  rate_2PCR = 0.8,
  nPCR1 = 16,
  nPCR2 = 10,
  LinearAmp = F,
  LinearAmp_coef = 2000,
  depth_mean,
  depth_sd,
  nbatch = 1
)

Arguments

SE	input, should be a summerized experiment rather than a list of elements, default is False
true_counts	gene cell matrix
meta_cell	the meta information related to cells, will be combined with technical cell level information and returned
protocol	a string, can be "nonUMI" or "UMI"
alpha_mean	the mean of rate of subsampling of transcripts during capture step, default at 10 percent efficiency
alpha_sd	the std of rate of subsampling of transcripts
lenslope	amount of length bias
nbins	number of bins for gene length
amp_bias_limit	range of amplification bias for each gene, a vector of length ngenes
rate_2PCR	PCR efficiency, usually very high, default is 0.8
nPCR1	the number of PCR cycles, default is 16
LinearAmp	if linear amplification is used for pre-amplification step, default is FALSE
LinearAmp_coef	the coeficient of linear amplification, that is, how many times each molecule is amplified by
depth_mean	mean of sequencing depth
depth_sd	std of sequencing depth
nbatch	number of batches
hge2true	if we add high gene expression to true counts

Galaxeee/TedSim documentation built on Oct. 2, 2022, 1:25 a.m.