perform_DEA: Perform Differential Expression Analysis This function is...

In duohongrui/simutils: Common functions used in data simulation and evaluation

Perform Differential Expression Analysis This function is used to perform DEA for single-cell RNA-seq data by QLF model in edgeR package including the cellular detection rate.

Description

Perform Differential Expression Analysis This function is used to perform DEA for single-cell RNA-seq data by QLF model in edgeR package including the cellular detection rate.

Usage

perform_DEA(data, group, method, species = NULL, verbose = TRUE)

Arguments

data	A matrix of gene expression profile.
group	Group(or cluster) assignment of every cells in columns of matrix.
method	Which DE method will be used? Choices: edgeRQLF, edgeRQLFDetRate, MASTcpmDetRate, MASTtpmDetRate, MASTcpm, MASTtpm, limmatrend, limmavoom, ttest and wilcox.
species	We only support human or mouse to choose the gene length data from simutils::hs_gene_length or simutils::mm_gene_length and normalize the data by TPM. Users must set this parameter when using MASTtpmDetRate, MASTtpm, ttest or wilcox method.
verbose	Whether the process massages are returned.

Value

A dataframe of DEA result.

References

Soneson C, Robinson M D. Bias, robustness and scalability in single-cell differential expression analysis. Nature methods, 2018, 15(4): 255-261. https://doi.org/10.1038/nmeth.4612 Github URL: https://github.com/csoneson/conquer_comparison

duohongrui/simutils documentation built on March 12, 2024, 8:40 p.m.