find_DE_genes: Find DE genes across a particular feature

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

Find DE genes across a particular feature

Usage

find_DE_genes(
  x,
  directory = NULL,
  group.by = "seurat_clusters",
  filename = NULL,
  label = "all",
  method = "group",
  assay = "RNA",
  slot_data = "data"
)

Arguments

x	a Seurat object
directory	where to save the computed markers
group.by	a column in the meta data to group the cell types
filename	the name of the data file. If NULL, it will be generated automatically in the format of '$directory/marker_list_$group.by_$label.csv'
method	either 'group' to run DE gene of one group with respect to the rest of the dataset using presto::wilcoxauc, or 'pairwise' to run DE gene between any possible pairs of groups using find_DE_pairwise. The pairwise option can be very computationally expensive.

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