Concrete subclass for SUSHI CountQC SummarizedExperiment outputs

Top-level rowData(se) carries feature annotations; there are no DE results. May include a presentFlag / isPresent assay used as the QC denominator.

Value

An R6 class generator; $new() returns an ExploreDatasetSE_CountQC object.

Details

Inherits the accessor contract from ExploreDataset via ExploreDatasetSE; overrides only .build_config() and .prep().

Super classes

ExploreDataset -> ExploreDatasetSE -> ExploreDatasetSE_CountQC

Methods

Public methods

• ExploreDatasetSE_CountQC$clone()

Inherited methods

• ExploreDataset$all_pathways()
• ExploreDataset$assay_label()
• ExploreDataset$background_expression()
• ExploreDataset$contrast_label()
• ExploreDataset$contrast_meta()
• ExploreDataset$contrasts()
• ExploreDataset$data_type()
• ExploreDataset$de_all()
• ExploreDataset$de_display_extras()
• ExploreDataset$enrichment_filter()
• ExploreDataset$enrichment_kinds()
• ExploreDataset$enrichment_table()
• ExploreDataset$factor_levels()
• ExploreDataset$factor_names()
• ExploreDataset$feature_display()
• ExploreDataset$feature_id_kind()
• ExploreDataset$feature_ids()
• ExploreDataset$format()
• ExploreDataset$has_assay()
• ExploreDataset$has_de()
• ExploreDataset$has_enrichment()
• ExploreDataset$has_pvalue()
• ExploreDataset$n_features()
• ExploreDataset$n_samples()
• ExploreDataset$omics_class()
• ExploreDataset$organism()
• ExploreDataset$primary_assay()
• ExploreDataset$primary_assay_name()
• ExploreDataset$primary_contrast()
• ExploreDataset$primary_grouping()
• ExploreDataset$proteomics_choices()
• ExploreDataset$raw_assay()
• ExploreDataset$raw_assay_name()
• ExploreDataset$ref_build()
• ExploreDataset$sample_factor()
• ExploreDataset$sample_ids()
• ExploreDataset$secondary_grouping()
• ExploreDataset$sgrna_to_gene()
• ExploreDataset$source()
• ExploreDatasetSE$assay()
• ExploreDatasetSE$assay_names()
• ExploreDatasetSE$backend()
• ExploreDatasetSE$backend_kind()
• ExploreDatasetSE$de()
• ExploreDatasetSE$enrichment()
• ExploreDatasetSE$enrichment_input()
• ExploreDatasetSE$features()
• ExploreDatasetSE$initialize()
• ExploreDatasetSE$samples()

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ExploreDatasetSE_CountQC$clone()

The objects of this class are cloneable with this method.

Usage

ExploreDatasetSE_CountQC$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

library(SummarizedExperiment)
de_result <- readRDS(system.file("examples/genomics/deResult.rds", package = "exploreDE"))
# A count table without DE results, as SUSHI's CountQC writes it
se <- SummarizedExperiment(
  assays = list(counts = assay(de_result, "counts")),
  colData = colData(de_result),
  rowData = rowData(de_result)[, c("gene_id", "gene_name", "description")]
)
eds <- ExploreDatasetSE_CountQC$new(se)
eds
#> <ExploreDatasetSE_CountQC  (se)>
#>   data_type:        CountQC
#>   feature_id_kind:  gene
#>   organism:         NA
#>   ref_build:        NA
#>   samples x features: 9 x 21057
#>   factors (1):
#>     Condition  (primary): diff, undiff
#>   contrasts (0): 
#>   primary_contrast: NA
#>   assays:           counts, vst
#>   enrichment:       (none)
eds$has_de()
#> [1] FALSE