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Find the upregulated DEGs for each cluster, comparing two clusters. As well as the conserved markers between them.

TS_Find_DEGs_and_overlap.Rd

Returns a list containing:

  • Upregulated markers in cluster 1 compared to cluster 2

  • Upregulated markers in cluster 2 compared to cluster 1

  • Shared markers between them, compared to all other clusters in the Seurat object

Depends on:

  • Seurat

  • magrittr

  • tidyverse

  • VennDetail

Automatically filters resulting DEG list so that '0 < p_val_adj > 0.05.

Usage

TS_Find_DEGs_and_overlap(
  seurat_object,
  ident.1,
  ident.2,
  grouping_variable_name = "tested_population",
  only_pos_markers = T,
  test_use = "wilcox",
  plot_venn = F,
  export_venn = F,
  filename_pdf = "Venn_output",
  width = 8.27,
  heigth = 5.83
)

Arguments

seurat_object

Your Seurat object

ident.1

Name of cluster 1

ident.2

Name of cluster 2

grouping_variable_name

Name of the combined group. Could be anything. Defaults to 'tested_population'.

only_pos_markers

Whether to only return positively upregulated markers for the specific cluster. Defaults to 'TRUE'

test_use

Statistical test used for DE testing. Defaults to 'Wilcoxon ranked sum test'.

plot_venn

Whether to plot a Venn diagram for the gene lists. Defaults to 'FALSE'

export_venn

Whether to export the Venn diagram to working directory. Defaults to 'FALSE'

filename_pdf

File name for exported Venn diagram.

width

Width of saved Venn diagram. Defaults to '8.27 inches', which is A5 landscape format.

height

Height of saved Venn diagram. Defaults to '5.83 inches', which is A5 landscape format.