Quick hack to enable some assay-level metadata filtering on SummarizedExperiment

subset_SummarizedExperiment.R

library(SummarizedExperiment)

## create a SummarizedExperiment
se <- SummarizedExperiment(assays = 
                             list(
                               counts = matrix(0:99, 10, 10), 
                               cpm = matrix(200:299, 10, 10)
                             )
                           )
## add tabular metadata with assay-specific properties
metadata(se) <- list(
  assay_metadata = DataFrame(
  property1 = c("A", "B"),
  property2 = c(3, 5),
  row.names = assayNames(se)
  )
)

## perform filtering at the assay level based on metadata
subset_by_assay <- function(se, property, value) {
  mse <- metadata(se)$assay_metadata
  ids <- mse[[property]] %in% value
  assays(se)[ids]
}

subset_by_assay(se, "property1", c("A", "B"))
#> List of length 2
#> names(2): counts cpm
subset_by_assay(se, "property1", "A")
#> List of length 1
#> names(1): counts
subset_by_assay(se, "property1", "B")
#> List of length 1
#> names(1): cpm

subset_by_assay(se, "property2", 3)
#> List of length 1
#> names(1): counts
subset_by_assay(se, "property2", 5)
#> List of length 1
#> names(1): cpm