Methods in this package operate on log-transformed (multiplicative scale) expression.
We attempt to check for this at construction, and then over-ride the assay method to return the "layer" containing such log-transformed data.
magic_assay_names()
assay_idx(x)
# S4 method for SingleCellAssay,missing
assay(x, i, withDimnames = TRUE, ...)SingleCellAssay
must be missing for this method to apply
A logical(1), indicating whether the
dimnames of the SummarizedExperiment object should be applied (i.e.
copied) to the extracted assays. More precisely, setting
withDimnames=FALSE in the getter returns the
assays as-is whereas setting withDimnames=FALSE
return them with possibly modified dimnames.
Setting withDimnames=FALSE in the setter (assays<-)
is required when the dimnames on the supplied assays are not identical
to the dimnames on the SummarizedExperiment object; it does not
influence actual assignment of dimnames to assays (they're always
stored as-is).
Note that
assays(x, withDimnames=FALSE) <- assays(x, withDimnames=FALSE)is guaranteed to always work and be a no-op. This is not the case
if withDimnames=TRUE is used or if withDimnames is
not specified.
passed to parent method
By default we return the assay whose names, as given by assayNames(x), matches the first element in the vector c('thresh', 'et', 'Et', 'lCount', 'logTPM', 'logCounts', 'logcounts').
magic_assay_names: list of names assumed to represent log-transformed data, in order of usage preference
assay_idx: what index is returned by default by `assay`
data(vbetaFA)
assay(vbetaFA)[1:3,1:3]
#> wellKey
#> primerid Sub01 1 A01 Sub01 1 A02 Sub01 1 A03
#> B3GAT1 0 0 0
#> BAX 0 0 0
#> BCL2 0 0 0
assay(vbetaFA, 'thresh', withDimnames = FALSE) = assay(vbetaFA)*0 - 9
assay(vbetaFA)[1:3, 1:3]
#> wellKey
#> primerid Sub01 1 A01 Sub01 1 A02 Sub01 1 A03
#> B3GAT1 -9 -9 -9
#> BAX -9 -9 -9
#> BCL2 -9 -9 -9