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() # S4 method for SingleCellAssay,missing assay(x, i, ...)
x |
|
---|---|
i | must be |
... | 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
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 0assay(vbetaFA, 'thresh') = 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