Description Usage Arguments Details Functions Examples
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.
1 2 3 4 5 6 | magic_assay_names()
assay_idx(x)
## S4 method for signature 'SingleCellAssay,missing'
assay(x, i, withDimnames = TRUE, ...)
|
x |
|
i |
must be |
withDimnames |
A Setting 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 |
... |
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'
1 2 3 4 |
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