get_module_score: Calculate the module score of KEGG pathway

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

It is extremely important to set seed for this function

Usage

get_module_score(
  x,
  save_path,
  all_path = NULL,
  pgenes = NULL,
  append_meta = F,
  regexp = "^X",
  species = "human",
  control_num = 50
)

Arguments

x	a Seurat object
save_path	where to save to output dataframe. It is recommended to save the results because this function tends to be time consuming.
all_path	a dataframe with pathway column being the comon pathway names, and the kegg_id column being the KEGG ID for the pathways
pgenes	a named list of vectors of genes
append_meta	if TRUE, a Seurat object will be created with the expression matrix being the module scores and metadata inherited from the input Seurat object. This output will be more convenient for doing violin plot and heatmap
regexp	remove a part of cell ID names that may arise because of some tidyverse manipulations. If NULL, no changes will happen

Value

a matrix or a Seurat object whose rows are gene module names in pgenes and whose columns are cell names

Yutong441/TBdev documentation built on Dec. 18, 2021, 8:22 p.m.