run_fgsea {scITD}

Run fgsea for one cell type of one factor

Description

Run fgsea for one cell type of one factor

Usage

run_fgsea(
  container,
  factor_select,
  ctype,
  db_use = "GO",
  signed = TRUE,
  min_gs_size = 15,
  max_gs_size = 500,
  ncores = container$experiment_params$ncores
)

Arguments

container

environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses

factor_select

numeric The factor of interest

ctype

character The cell type of interest

db_use

character The database of gene sets to use. Database options include "GO", "Reactome", "KEGG", "BioCarta", and "Hallmark". More than one database can be used. (default="GO")

signed

logical If TRUE, uses signed gsea. If FALSE, uses unsigned gsea. Currently only works with fgsea method. (default=TRUE)

min_gs_size

numeric Minimum gene set size (default=15)

max_gs_size

numeric Maximum gene set size (default=500)

ncores

numeric The number of cores to use (default=container$experiment_params$ncores)

Value

A data.frame of the fgsea results for enrichment of gene sets in a given cell type for a given factor. The results contain adjusted p-values, normalized enrichment scores, leading edge genes, and other information output by fgsea.