magic_assay_names {MAST} | R Documentation |
assay
returnedMethods 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 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'
data(vbetaFA) assay(vbetaFA)[1:3,1:3] assay(vbetaFA, 'thresh', withDimnames = FALSE) = assay(vbetaFA)*0 - 9 assay(vbetaFA)[1:3, 1:3]