Assay
MethodsMethods for Assay
objects for generics defined in
other packages
# S3 method for Assay
[(x, i, j, ...)# S3 method for Assay
[[(x, i, ..., drop = FALSE)
# S3 method for Assay
dim(x)
# S3 method for Assay
dimnames(x)
# S3 method for Assay
merge(x = NULL, y = NULL, add.cell.ids = NULL, merge.data = TRUE, ...)
# S3 method for Assay
subset(x, cells = NULL, features = NULL, ...)
# S4 method for Assay
[[(x, i, j, ...) <- value
# S4 method for Assay
colMeans(x, na.rm = FALSE, dims = 1, ..., slot = "data")
# S4 method for Assay
colSums(x, na.rm = FALSE, dims = 1, ..., slot = "data")
# S4 method for Assay
rowMeans(x, na.rm = FALSE, dims = 1, ..., slot = "data")
# S4 method for Assay
rowSums(x, na.rm = FALSE, dims = 1, ..., slot = "data")
# S4 method for Assay
show(object)
An Assay
object
For [[
: metadata names; for all other methods,
feature names or indices
Cell names or indices
Arguments passed to other methods
See drop
A vector or list of one or more objects to merge
A character vector of length(x = c(x, y))
;
appends the corresponding values to the start of each objects' cell names
Merge the data slots instead of just merging the counts (which requires renormalization); this is recommended if the same normalization approach was applied to all objects
Additional metadata to add
logical. Should missing values (including NaN
)
be omitted from the calculations?
completely ignored by the Matrix
methods.
Name of assay expression matrix to calculate column/row means/sums on
[
: The data
slot for features i
and cells
j
[[
: The feature-level metadata for i
dim
: The number of features (nrow
) and cells
(ncol
)
dimnames
: Feature (row) and cell (column) names
merge
: Merged object
subset
: A subsetted Assay
[[<-
: x
with metadata value
added as i
colMeans
: The column (cell-wise) means of slot
colSums
: The column (cell-wise) sums of slot
rowMeans
: The row (feature-wise) means of slot
rowSums
: The row (feature-wise) sums of slot
show
: Prints summary to stdout
and
invisibly returns NULL
[.Assay
: Get expression data from an Assay
[[.Assay
: Get feature-level metadata
dim.Assay
: Number of cells and features for an Assay
dimnames.Assay
: Cell- and feature-names for an Assay
merge.Assay
: Merge Assay
objects
subset.Assay
: Subset an Assay
[[<-,Assay-method
: Add feature-level metadata
colMeans,Assay-method
: Calculate colMeans
on an
Assay
colSums,Assay-method
: Calculate colSums
on an
Assay
rowMeans,Assay-method
: Calculate rowMeans
on an
Assay
rowSums,Assay-method
: Calculate rowSums
on an
Assay
show,Assay-method
: Overview of an Assay
object