amplify_1cell: This function simulates the amplification, library prep, and...

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

This function simulates the amplification, library prep, and the sequencing processes.

Description

This function simulates the amplification, library prep, and the sequencing processes.

Usage

amplify_1cell(
  true_counts_1cell,
  protocol,
  rate_2cap,
  gene_len,
  amp_bias,
  rate_2PCR,
  nPCR1,
  nPCR2,
  LinearAmp,
  LinearAmp_coef,
  N_molecules_SEQ
)

Arguments

true_counts_1cell	the true transcript counts for one cell (one vector)
protocol	a string, can be "nonUMI" or "UMI"
rate_2cap	the capture efficiency for this cell
gene_len	gene lengths for the genes/transcripts, sampled from real human transcript length
amp_bias	amplification bias for each gene, a vector of length ngenes
rate_2PCR	PCR efficiency, usually very high
nPCR1	the number of PCR cycles
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
N_molecules_SEQ	number of molecules sent for sequencing; sequencing depth

Value

read counts (if protocol="nonUMI") or UMI counts (if protocol="UMI)

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