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SeuratObject (version 4.0.1)

DimReduc-methods: DimReduc Methods

Description

Methods for DimReduc objects for generics defined in other packages

Usage

# S3 method for DimReduc
[(x, i, j, drop = FALSE, ...)
# S3 method for DimReduc
[[(x, i, j, drop = FALSE, ...)
# S3 method for DimReduc
dim(x)
# S3 method for DimReduc
dimnames(x)
# S3 method for DimReduc
length(x)
# S3 method for DimReduc
merge(x = NULL, y = NULL, add.cell.ids = NULL, ...)
# S3 method for DimReduc
names(x)
# S3 method for DimReduc
print(x, dims = 1:5, nfeatures = 20, projected = FALSE, ...)
# S3 method for DimReduc
subset(x, cells = NULL, features = NULL, ...)
# S4 method for 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