save_DE_genes: Save Differentially Expressed Genes

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

This function intends to save DE genes for presentation and publication but not for computing. For downstream analysis, the find_DE_genes function would be able to save the raw output.

Usage

save_DE_genes(
  x,
  save_dir,
  markers = NULL,
  group.by = "revised",
  label = "all",
  save_format = "excel",
  weighting = "logFC",
  cluster = "group",
  gene = "feature",
  show_num = 30,
  value = "avgExpr",
  AP = NULL,
  organism_db = NULL
)

Arguments

x	a Seurat object
save_dir	where to save the results
group.by	a column in the meta data to group the cell types
label	the file name would be: '$save_dir/DE_$group.by_$label.$suffix'
save_format	can be 'excel' or 'gene_table' for average expression only
weighting	which column to arrange the genes from top to bottom
gene	which column stores the gene names
show_num	how many DE genes to save per group. If 'all', everything will be saved
value	which column stores the average expression
AP	a list that contains the cell_order entry to arrange the cells
organism_db	a genome database, e.g. org.Hs.eg.db. It is optional unless you would like to add a ensemble ID column

See Also

find_DE_genes

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