SeuratObject: DimReduc-methods – R documentation

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SeuratObject

DimReduc-methods

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