XYomics (version 0.1.2)

sex_stratified_analysis_sc: Compute sex-specific differentially expressed genes (DEGs)

Description

Identifies differentially expressed genes (DEGs) separately for male and female samples within different cell types using the Seurat package. Compares gene expression between control and perturbed groups in each sex.

Usage

sex_stratified_analysis_sc(
  seurat_obj,
  sex_column = "sex",
  phenotype_column = "status",
  celltype_column = "cell_type",
  sex_labels_vector = c("F", "M"),
  min_logfc = 0.25,
  phenotype_labels_vector = c("WT", "TG"),
  method = "wilcox"
)

Value

A list with male and female DEGs results.

Arguments

seurat_obj

Seurat object containing the single-cell data.

sex_column

Character. Column name in metadata for sex (default "sex").

phenotype_column

Character. Column name in metadata for phenotype (default "status").

celltype_column

Character. Column name in metadata for cell type (default "cell_type").

sex_labels_vector

Character vector of sex labels (default c("F","M")).

min_logfc

Numeric. Minimum absolute log fold change threshold (default 0.25).

phenotype_labels_vector

Character vector of phenotype groups (default c("WT","TG")).

method

Character. Statistical test to use for differential expression (default "wilcox").