calculate_DEGs_properties: Summarize the Ability of Simulating DEGs

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

Summarize the Ability of Simulating DEGs

Description

Summarize the Ability of Simulating DEGs

Usage

calculate_DEGs_properties(
  count_matrix,
  group,
  DEGs,
  DEA_method,
  model_method,
  verbose = TRUE
)

Arguments

count_matrix	A matrix or a list with names of gene expression data.
group	A vector of characters which indicate which group a cell belongs to. A list is also supported when many matrices of data is input in count_matrix parameter.
DEGs	A list of DEGs with the names of xxxvsxxx. Note that the names of DEGs are in the rownames of the matrix or the dataframe and the names of xxx is in the group characters. If you have input the lists of group and count_matrix, the every sub-list in DEGs list should match with every data in count_matrix and group at the same index or position.
DEA_method	The DEA method to get the DEGs. Choices: edgeRQLF, edgeRQLFDetRate, MASTcpmDetRate, MASTtpmDetRate, MASTcpm, MASTtpm, limmatrend, limmavoom, ttest and wilcox.
model_method	The method to establish the model. SVM, Decision tree or RF (Random Forest).
verbose	Whether the process massages are returned.

Value

A list

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