postprocess_marker_variables: Find the marker genes the separate one cell type from all...

In linnykos/multiomicCCA: Tilted CCA

Find the marker genes the separate one cell type from all other cell types

Description

Based on the output of tiltedCCA::differential_expression, for a particular cell type, 1) when comparing against every other cell type, find all the variables that have an adjusted p-value smaller than p_val_thres and also have a log fold change larger than log_thres_name, and 2) if the variable was selected for more than num_quantile_threshold percentage of the comparisons with other cell types, we deem it as a marker gene for this cell type.

Usage

postprocess_marker_variables(
  de_list,
  log_thres_name = "avg_log2FC",
  log_thres = 2,
  num_quantile_threshold = 0.25,
  p_val_name = "p_val",
  p_val_adj_name = "p_val_adj",
  p_val_thres = 1e-04
)

Arguments

de_list	output of the tiltedCCA::differential_expression function
log_thres_name	character of the column in each of de_list$de_list for the log fold change
log_thres	positive value, for selecting variables with log fold change larger than log_thres
num_quantile_threshold	value between 0 and 1
p_val_name	character of the column in each of de_list$de_list for the p-value
p_val_adj_name	character of the column in each of de_list$de_list for the multiple-testing adjusted p-value
p_val_thres	small positive value between 0 and 1, for selecting variables with p-values smaller than p_val_thres

Value

a list of variable vectors, one vector for each element in de_list$level_vec

linnykos/multiomicCCA documentation built on July 17, 2025, 3:16 a.m.