magic_assay_names {MAST} | R Documentation

## Default `assay` returned

### Description

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.

### Usage

    magic_assay_names()

    assay_idx(x)

    ## S4 method for signature 'SingleCellAssay,missing'
    assay(x, i, withDimnames = TRUE, ...)

### Arguments

`x` | `SingleCellAssay`
`i` | must be `missing` for this method to apply
`withDimnames` | 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

### 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

- `assay_idx`: what index is returned by default by 'assay'

### Examples

    data(vbetaFA)
    assay(vbetaFA)[1:3,1:3]
    assay(vbetaFA, 'thresh', withDimnames = FALSE) = assay(vbetaFA)*0 - 9
    assay(vbetaFA)[1:3, 1:3]

[Package MAST version 1.16.0 Index]