inst/test_rds_files/make_test_rds_files.R

In CRI-iAtlas/iatlas.modules2: iAatlas Modules2

cnf1 <- CohortNumericFilter$new(
  "name" = "B_cells_Aggregate2",
  "min" = 0,
  "max" = .01
)

cnf2 <- CohortNumericFilter$new(
  "name" = "Neutrophils_Aggregate2",
  "min" = 0,
  "max" = .1
)

cnfs1 <- CohortFilterList$new(list(), type = "numeric")
cnfs2 <- CohortFilterList$new(list(cnf1), type = "numeric")

cgf1 <- CohortGroupFilter$new(
  "name" = "PCAWG_Study",
  "values" = c("BLCA-US", "BRCA-US", "CLLE-ES")
)

cgf2 <- CohortGroupFilter$new(
  "name" = "Immune_Subtype",
  "values" = c("C4", "C5", "C6")
)

cgfs1 <- CohortFilterList$new(list(), type = "group")
cgfs2 <- CohortFilterList$new(list(cgf2), type = "group")


cf1 <- CohortFilters$new(
  numeric_filters = cnfs1,
  group_filters = cgfs1
)

cf2 <- CohortFilters$new(
  numeric_filters = cnfs2,
  group_filters = cgfs2
)

tag_group1 <- TagGroup$new(
  dataset_names = "PCAWG", group_name = "Immune_Subtype"
)

tag_group2 <- TagGroup$new(
  dataset_names = "TCGA", group_name = "Immune_Subtype"
)

tag_group3 <- TagGroup$new(
  dataset_names = c("Gide_Cell_2019", "HugoLo_IPRES_2016"), group_name = "Responder"
)

tag_group4 <- TagGroup$new(
  dataset_names = "TCGA", group_name = "TCGA_Study"
)

mutation_group <- MutationStatusGroup$new(
  dataset_names = "TCGA", mutation_name = "ABL1:(NS)"
)

bin_group <- FeatureBinGroup$new(
  dataset_names = "TCGA", feature_name = "B_cells_Aggregate2", feature_bins = 2
)

objects <- list(
  "pcawg_immune_subtype_cohort_obj" = Cohort$new(
    "filter_object" = cf1,
    "group_object" = tag_group1
  ),

  "tcga_immune_subtype_cohort_obj" = Cohort$new(
    "filter_object" = cf1,
    "group_object" = tag_group2
  ),

  "tcga_immune_subtype_cohort_obj_small" = Cohort$new(
    "filter_object" = cf2,
    "group_object" = tag_group2
  ),

  "tcga_tcga_study_cohort_obj" = Cohort$new(
    "filter_object" = cf1,
    "group_object" = tag_group4
  ),

  "ici_responder_cohort_obj" = Cohort$new(
    "filter_object" = cf1,
    "group_object" = tag_group3
  ),

  "tcga_mutation_cohort_obj_small" = Cohort$new(
    "filter_object" = cf2,
    "group_object" = mutation_group
  ),

  "tcga_bin_cohort_obj_small" = Cohort$new(
    "filter_object" = cf2,
    "group_object" = bin_group
  ),

  "upload_cohort_obj" = UploadCohort$new(
    "upload_tbl" =  readr::read_csv(file.path(
      system.file("csv", package = "iatlas.modules2"),
      "test_user_group.csv"
    )),
    "group_name" = "COAD"
  )
)

files <- stringr::str_c(
  "inst/test_rds_files/",
  names(objects),
  ".rds"
)

purrr::walk2(
  objects,
  files,
  saveRDS,
  version = 2
)