Assign genes into dynamic groups based on expression, correlation, and CV

This function identifies gene behavior patterns (Up, Down, Stable, fluctuated, Low expression) based on: - time-course correlation - differential expression - mean expression - coefficient of variation (CV)

Usage

se2gene_group(
  se,
  assay_name = "conc",
  group_by = "condition",
  min_expresion_threhold = 1,
  CV_with_time_threhold = 0.1,
  padj_threhold = 0.05,
  k_cluster = 10
)

Arguments

se

A SummarizedExperiment object.

assay_name

Assay name to use (default "conc").

group_by

Column in colData(se) defining sample ordering.

min_expresion_threhold

Minimum mean expression.

CV_with_time_threhold

CV threshold used to define stable genes.

padj_threhold

Adjusted p-value threshold for DEGs.

k_cluster

Number of clusters for mufzz

Value

Updated SummarizedExperiment with gene grouping added to rowData.