R: 'DimReduc' Methods

DimReduc-methods {SeuratObject} | R Documentation

## `DimReduc` Methods

### Description

Methods for `DimReduc` objects for generics defined in other packages

### Usage

    ## S3 method for class 'DimReduc'
    x[i, j, drop = FALSE, ...]

    ## S3 method for class 'DimReduc'
    x[[i, j, drop = FALSE, ...]]

    ## S3 method for class 'DimReduc'
    dim(x)

    ## S3 method for class 'DimReduc'
    dimnames(x)

    ## S3 method for class 'DimReduc'
    length(x)

    ## S3 method for class 'DimReduc'
    merge(x = NULL, y = NULL, add.cell.ids = NULL, ...)

    ## S3 method for class 'DimReduc'
    names(x)

    ## S3 method for class 'DimReduc'
    print(x, dims = 1:5, nfeatures = 20, projected = FALSE, ...)

    ## S3 method for class 'DimReduc'
    subset(x, cells = NULL, features = NULL, ...)

    ## S4 method for signature 'DimReduc'
    show(object)

### Arguments

`x, object` | A `DimReduc` object
`i` | For `[`: feature names or indices; for `[[`: cell names or indices
`j` | Dimensions to pull for
`drop` | See `drop`
`...` | Arguments passed to other methods
`y` | A vector or list of one or more objects to merge
`add.cell.ids` | A character vector of `length(x = c(x, y))`; appends the corresponding values to the start of each objects' cell names
`dims` | Number of dimensions to display
`nfeatures` | Number of genes to display
`projected` | Use projected slot
`cells, features` | Cells and features to keep during the subset

### Value

`[`: Feature loadings for features `i` and dimensions `j`

`[[`: Cell embeddings for cells `i` and dimensions `j`

`dim`: The number of cells (`nrow`) and dimensions (`ncol`)

`dimnames`: The cell (row) and dimension (column) names

`length`: The number of dimensions

`names`: The names for the dimensions (eg. “PC_1”)

`print`: Displays set of features defining the components and invisibly returns `x`

`subset`: `x` for cells `cells` and features `features`

`show`: Prints summary to `stdout` and invisibly returns `NULL`

### Functions

- `[.DimReduc`: Pull feature loadings

- `[[.DimReduc`: Pull cell embeddings

- `dim.DimReduc`: The number of cells and dimensions for a `DimReduc`

- `dimnames.DimReduc`: The cell and dimension names for a `DimReduc` object

- `length.DimReduc`: The number of dimensions for a `DimReduc` object

- `merge.DimReduc`: Merge two or more `DimReduc` objects together

- `names.DimReduc`: The dimension names for a `DimReduc` object

- `print.DimReduc`: Prints a set of features that most strongly define a set of components; note: requires feature loadings to be present in order to work

- `subset.DimReduc`: Subset a `DimReduc` object

- `show,DimReduc-method`: Show basic summary of a `DimReduc` object

### See Also

`cat`

[Package SeuratObject version 4.0.3 Index]