R/s4_class.R

In timothy-barry/sceptre: Analysis of Single-Cell CRISPR Screen Data

# class union
#' @import Matrix
# setClassUnion("grna_matrix_class", c("matrix", "dgCMatrix", "dgRMatrix", "dgTMatrix", "lgCMatrix", "lgRMatrix", "lgTMatrix"))
# setClassUnion("response_matrix_class", c("matrix", "dgCMatrix", "dgRMatrix", "dgTMatrix"))


# sceptre object class
setClass("sceptre_object",
  slots = list(
    # raw data
    response_matrix = "list",
    grna_matrix = "list",
    covariate_data_frame = "data.frame",
    covariate_matrix = "matrix",
    grna_target_data_frame = "data.frame",
    low_moi = "logical",
    covariate_names = "character",

    # analysis parameters
    discovery_pairs = "data.frame",
    positive_control_pairs = "data.frame",
    formula_object = "formula",
    side_code = "integer",
    resampling_approximation = "character",
    control_group_complement = "logical",
    run_permutations = "logical",
    n_nonzero_trt_thresh = "integer",
    n_nonzero_cntrl_thresh = "integer",
    B1 = "integer", B2 = "integer", B3 = "integer",
    grna_integration_strategy = "character",
    grna_assignment_method = "character",
    grna_assignment_hyperparameters = "list",
    multiple_testing_alpha = "numeric",
    multiple_testing_method = "character",
    cell_removal_metrics = "integer",
    cellwise_qc_thresholds = "list",

    # computed objects
    mitochondrial_gene = "logical",
    M_matrix = "matrix",
    n_nonzero_tot_vector = "integer",
    discovery_pairs_with_info = "data.frame",
    positive_control_pairs_with_info = "data.frame",
    negative_control_pairs = "data.frame",
    initial_grna_assignment_list = "list",
    grna_assignments_raw = "list",
    grna_assignments = "list",
    grnas_per_cell = "integer",
    cells_w_zero_or_twoplus_grnas = "integer",
    cells_in_use = "integer",
    n_discovery_pairs = "integer",
    n_ok_discovery_pairs = "integer",
    n_positive_control_pairs = "integer",
    n_ok_positive_control_pairs = "integer",
    calibration_group_size = "integer",
    n_calibration_pairs = "integer",
    import_grna_assignment_info = "list",
    mean_cells_per_grna = "numeric",

    # cached objects
    response_precomputations = "list",

    # flags
    last_function_called = "character",
    functs_called = "logical",

    # results
    calibration_result = "data.frame",
    power_result = "data.frame",
    discovery_result = "data.frame",

    # odm-related entries
    nuclear = "logical",
    nf_pipeline = "logical",
    integer_id = "integer",
    elements_to_analyze = "character"
  )
)