amplify_cell: Simulate amplification, library prep, and the sequencing...

Description Usage Arguments Value References

View source: R/esco-simulate.R

Description

Simulate amplification, library prep, and the sequencing processes. (This function is borrowed from SymSim).

Usage

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amplify_cell(true_counts_1cell, 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)

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

nPCR2

the number of second 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

UMI counts

References

Zhang X, Xu C, Yosef N. Simulating multiple faceted variability in single cell RNA sequencing. Nature communications. 2019 Jun 13;10(1):1-6. https://www.nature.com/articles/s41467-019-10500-w


JINJINT/splattermodify documentation built on May 19, 2021, 4:05 p.m.