SimpleListSparseAssays-class: SimpleListSparseAssays objects

In PeteHaitch/SparseSummarizedExperiment: SparseSummarizedExperiment Container

Description

A concrete subclass of the SparseAssays virtual class. As such, all the methods documented in ?SparseAssays also work on a SimpleListSparseAssays object. See SparseAssays for details.

Usage

## S4 method for signature 'SimpleListSparseAssays'
dim(x)

## S4 method for signature 'SimpleListSparseAssays'
dimnames(x)

## S4 method for signature 'SimpleListSparseAssays,ANY'
x[i, j, ..., drop = FALSE]

## S4 replacement method for signature 'SimpleListSparseAssays,ANY,ANY,ANY'
x[i, j, ...] <- value

## S4 method for signature 'SimpleListSparseAssays'
rbind(..., deparse.level = 1)

## S4 method for signature 'SimpleListSparseAssays'
cbind(..., deparse.level = 1)

## S4 method for signature 'SimpleListSparseAssays,SimpleListSparseAssays'
combine(x, y, ...)

Arguments

x	A SimpleListSparseAssays object.
i, j	Numeric or character vectors indicating which rows of the sparse assays (i) and samples (j) to select.
...	For cbind(), rbind(), and combine() one or more SimpleListSparseAssay objects. Otherwise, additional arguments, for use in specific methods.
drop	Not used by [,SimpleListSparseAssays,ANY-method.
value	An object of a class specified in the S4 method signature or as outlined in ‘Details’.
deparse.level	See ?base::cbind for a description of this argument.
y	A SimpleListSparseAssays object.

Details

The SimpleListSparseAssays class has a nested-list structure. This hierarchy is illustrated below for an example with two sparse assays and three samples:

SimpleListSparseAssays
|-- sparse_assay_1
|   |-- sample_1
|   |   |-- key
|   |   |-- value
|   |-- sample_2
|   |   |-- key
|   |   |-- value
|   |-- sample_3
|   |   |-- key
|   |   |-- value
|-- sparse_assay_2
|   |-- sample_1
|   |   |-- key
|   |   |-- value
|   |-- sample_2
|   |   |-- key
|   |   |-- value
|   |-- sample_3
|   |   |-- key
|   |   |-- value

Each ‘key’ is an integer vector and all key elements must have identical length. Each ‘value’ element is a matrix object. Each value element may have a different number of rows but the maximum number of rows must be less than or equal to the length of the key elements. A row of the value element may be pointed to multiple times by the key element within the same sample and asssay.

Author(s)

Peter Hickey, [e-mail]

See Also

• SparseAssays objects for a description of the available methods.

Examples

# TODO: Get old examples from docs?
# TODO: Use SparseAssays(matrix) in examples?
# TODO: Set names on 'key' elements so that can demonstrate combine().
## ---------------------------------------------------------------------
## DIRECT MANIPULATION OF SparseAssays OBJECTS
## ---------------------------------------------------------------------
sl1 <- SimpleList(
  s1 = SimpleList(key = as.integer(c(NA, 1, NA, NA, 2, NA, 3, NA, 4, 5)),
                  value = matrix(1:10, ncol = 2)),
  s2 = SimpleList(key = as.integer(c(NA, NA, 1, 2, NA, NA, 3, 4, NA, NA)),
                  value = matrix(8:1, ncol = 2)))

sl2 <- SimpleList(
  s1 = SimpleList(key = as.integer(c(NA, 1, NA, 2, 2, NA, 1, NA, NA, 1)),
                  value = matrix(1:2, ncol = 1)),
  s2 = SimpleList(key = as.integer(c(1, 1, 1, 2, NA, NA, NA, NA, NA, NA)),
                  value = matrix(4:3, ncol = 1)))
sa <- SparseAssays(SimpleList(sa1 = sl1, sa2 = sl2))
sa

as(sa, "SimpleList")

length(sa)
sa[[2]]
dim(sa)

sa2 <- sa[-4, 2]
sa2
length(sa2)
sa2[[2]]
dim(sa2)
dimnames(sa2)

names(sa)
names(sa) <- c("sa1", "sa2")
names(sa)
sa[["sa2"]]

rbind(sa, sa)
## Not run: 
  # ERROR: cbind-ing requires unique sample names
  cbind(sa, sa)

## End(Not run)
# Works because unique sample names
cbind(sa[, 1], sa[, 2])
## Not run: 
  # ERROR: combine() requires named 'key' elements
  combine(sa[1:7, 1], sa[3:8, 1])
  # ERROR: combine() requires named 'key' elements
  combine(sa[1:7, 1], sa[3:8, 2])

## End(Not run)
# TODO: An example of combine() that works because keys are named.

PeteHaitch/SparseSummarizedExperiment documentation built on May 8, 2019, 1:31 a.m.