script.r

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

dir.create("inst/extdata", recursive = T)

usethis::use_data(egSymbols)
usethis::use_data(goegs)
usethis::use_data(hsGO_BP)
usethis::use_data(score_RRS_result)
usethis::use_data(demo_gsea_df_all)
usethis::use_data(get_Formula_result)
get_Formula_result = formula_list

usethis::use_pipe() #在R中使用管道符
usethis::use_package("RColorBrewer", type = "Imports",
                     min_version = "1.1.2")
usethis::use_package("pheatmap", type = "suggests",
                     min_version = "1.0.12")
packageVersion("pheatmap")




devtools::document()
devtools::check()
devtools::load_all()

styler::style_pkg()
usethis::use_readme_rmd()
# devtools::install_github("lishensuo/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)
library(M2D)
?find_disease_pw
?score_RRS
sle_pw <- "GO:0001501"
sle_mol <- "CGP-20712"
vis_tern_one(
  score_RRS = score_RRS_result,
  sle_pw = sle_pw,
  sle_mol = sle_mol
)