find_disease_pw: find enriched GO_BP pathways related disease
In lishensuo/M2D: find Molecule(s) to Disease by reverse transcriptome

Description Usage Arguments Value Examples

find enriched GO_BP pathways related disease

find_disease_pw(
  m2dObj,
  n_degs = 500,
  p_deg = 0.05,
  pathway = "GOBP",
  n_terms = 10,
  p_term = 0.05,
  uncor_GOBP = TRUE,
  uncor_cut = 0.6,
  user_gobp = NULL
)

`m2dObj`	raw m2dObj
`n_degs`	how many disease degs to enrich
`p_deg`	signifcant disease degs cutoff
`pathway`	one of c("GOBP","user_gobp")
`n_terms`	how many disease related pathway
`p_term`	significant enriched degs
`uncor_GOBP`	wheather independent pathway
`uncor_cut`	correlation cutoff of independent pathway
`user_gobp`	GO BP ids

a list of disease-pathway-info.

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
)
disease_pw_list <- find_disease_pw(m2dObj)
disease_pw <- disease_pw_list$term_df
table(disease_pw$Term)
head(disease_pw)
enrich_raw <- disease_pw_list$enrich_raw@result
enrich_raw[1:4, 1:4]