Accessors functions — accessors • omXplore

Functions used to access the additional plots in the instances of the class MultiAssayExperiment.

get_adjacencyMatrix(object, ...)

# S4 method for class 'SummarizedExperiment'
get_adjacencyMatrix(object)

get_design(object, ...)

# S4 method for class 'MultiAssayExperiment'
get_design(object)

get_group(object, ...)

# S4 method for class 'MultiAssayExperiment'
get_group(object)

get_metacell(object, ...)

# S4 method for class 'SummarizedExperiment'
get_metacell(object, slot.name = c("metacell", "qMetacell"))

get_cc(object, ...)

# S4 method for class 'SummarizedExperiment'
get_cc(object)

get_parentProtId(object, ...)

# S4 method for class 'SummarizedExperiment'
get_parentProtId(object)

get_colID(object, ...)

# S4 method for class 'SummarizedExperiment'
get_colID(object)

get_type(object, ...)

# S4 method for class 'SummarizedExperiment'
get_type(object)

get_pkg_version(object, ...)

# S4 method for class 'SummarizedExperiment'
get_pkg_version(object)

Arguments

object: An instance of class SummarizedExperiment.
...: Additional parameters
slot.name: The name of the slot dedicated to cell metadata to search. Default values are 'metacell' and 'qMetacell'

Value

See individual method description for the return value.

If exists, the slot value requested.

A DataFrame containing the adjacency matrix of the dataset

A data.frame containing the metadata of the dataset

Examples


## -----------------------------------
## Accessing slots from a MSnSet dataset
## -----------------------------------
data(sub_R25)
se1 <- sub_R25[[1]]
parentProtId <- get_parentProtId(se1)
colID <- get_colID(se1)
type <- get_type(se1)
metacell <- get_metacell(se1)
conds <- get_group(sub_R25)