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

In YosefLab/SymSim: Simulate Single Cell RNA Sequencing Data

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)

YosefLab/SymSim documentation built on Sept. 30, 2024, 2:22 p.m.