Default assay returned

Source: R/SingleCellAssay-methods.R

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, ...)

Arguments

x

SingleCellAssay
i

must be missing for this method to apply
...

passed to parent method

Details

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').

Functions

  • magic_assay_names: list of names assumed to represent log-transformed data, in order of usage preference

Examples

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') = 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