gsea_disease_set: gsea enrichment analysis for disease up/down geneset to...

In lishensuo/M2D: find Molecule(s) to Disease by reverse transcriptome

Description

gsea enrichment analysis for disease up/down geneset to molecules signature

Usage

gsea_disease_set(
  m2dObj,
  p_deg = 0.05,
  n_degs = 500,
  p_both = 0.05,
  p_single = 0.01,
  demo = FALSE
)

Arguments

m2dObj	raw m2d object
p_deg	significant deg cutoff
n_degs	disease gene sets size
p_both	cutoff for both enrichment
p_single	cutoff for single enrichment
demo	gsea result for demo use to save time

Value

significant molecules that disease up/down geneset can enrich

Examples

library(M2D)
dir_disease <- system.file("extdata",
  "demo_BRCA_disease.csv",
  package = "M2D"
)
disease <- read.csv(dir_disease)
dir_molecule <- system.file("extdata",
  "demo_molecules_321_12320.csv",
  package = "M2D"
)
molecules <- data.table::fread(dir_molecule,
  data.table = FALSE
) %>%
  tibble::column_to_rownames("V1")
m2dObj <- list(
  disease = disease,
  molecule = molecules
)

enrich_double_list <- gsea_disease_set(
  m2dObj = m2dObj,
  demo = TRUE
)
enrich_double <- enrich_double_list$gsea_sig
dim(enrich_double)
unique(enrich_double$molecule)

lishensuo/M2D documentation built on Jan. 4, 2022, 9:44 a.m.