Generate summary of specific pathways and top contributing genes given an annotation

Generate summary of specific pathways and top contributing genes given an annotation

generate_summary_specific_modules(
  PCA_object,
  file = NULL,
  meta,
  annot_name,
  top_genes = 10,
  min_contrib = 0.1
)

Arguments

PCA_object

List, output from run_activity_analysis().

file

Character, path to file if you want the analysis stored as xlsx file with one sheet by cluster.

meta

Dataframe containing metadata, with cell labels as rownames.

annot_name

Character, name of the column in meta that should be used as annotation for cells.

top_genes

Integer, number of top genes contributing to PC to print.

min_contrib

Double, minimum contribution/weight of a gene to the PC. It overrides top_genes parameter and only top_genes contributing above min_contrib will be printed.

noise

Double, value between 0 and 1 indicating the maximum specificity you allow a non-specific cluster to have. Can be increased if no pathways appear as specific.

Value

List, one assay by cluster defined by annotation, and each displaying a table with the pathway, the top contributing genes and the pathway specificity.