Split TreeSummarizedExperiment column-wise or row-wise based on grouping variable

Source: R/splitOn.R

Split TreeSummarizedExperiment column-wise or row-wise based on grouping variable

splitOn(x, ...)

# S4 method for class 'SummarizedExperiment'
splitOn(x, group = f, f = NULL, ...)

# S4 method for class 'SingleCellExperiment'
splitOn(x, group = f, f = NULL, ...)

# S4 method for class 'TreeSummarizedExperiment'
splitOn(
  x,
  group = f,
  f = NULL,
  update.tree = update_rowTree,
  update_rowTree = FALSE,
  ...
)

unsplitOn(x, ...)

# S4 method for class 'list'
unsplitOn(x, update.tree = update_rowTree, update_rowTree = FALSE, ...)

# S4 method for class 'SimpleList'
unsplitOn(x, update.tree = update_rowTree, update_rowTree = FALSE, ...)

# S4 method for class 'SingleCellExperiment'
unsplitOn(
  x,
  altexp = altExpNames,
  altExpNames = names(altExps(x)),
  keep.dimred = keep_reducedDims,
  keep_reducedDims = FALSE,
  ...
)

Arguments

x

TreeSummarizedExperiment.

...

Arguments passed to agglomerateByVariable function for SummarizedExperiment objects and other functions. See agglomerateByVariable for more details.

  • use.names: Logical scalar. Specifies whether to name elements of list by their group names. (Default: TRUE)

group

Character scalar, character vector or factor vector. A column name from rowData(x) or colData(x) or alternatively a vector specifying how the merging is performed. If vector, the value must be the same length as nrow(x)/ncol(x). Rows/Cols corresponding to the same level will be merged. If length(levels(group)) == nrow(x)/ncol(x), x will be returned unchanged. If group matches with both dimensions, by must be specified. (Default: NULL)

f

Deprecated. Use group instead.

update.tree

Logical scalar. Should rowTree() also be merged? (Default: FALSE)

update_rowTree

Deprecated. Use update.tree instead.

altexp

Character vector. Specify the alternative experiments to be unsplit. (Default: names(altExps(x)))

altExpNames

Deprecated. Use altexp instead.

keep.dimred

Logical scalar. Should the reducedDims(x) be transferred to the result? Please note, that this breaks the link between the data used to calculate the reduced dims. (Default: FALSE)

keep_reducedDims

Deprecated. Use keep.dimred instead.

Value

For splitOn: SummarizedExperiment objects in a SimpleList.

For unsplitOn: x, with rowData and assay data replaced by the unsplit data. colData of x is kept as well and any existing rowTree is dropped as well, since existing rowLinks are not valid anymore.

Details

splitOn split data based on grouping variable. Splitting can be done column-wise or row-wise. The returned value is a list of SummarizedExperiment objects; each element containing members of each group.

Examples

data(GlobalPatterns)
tse <- GlobalPatterns
# Split data based on SampleType. 
se_list <- splitOn(tse, group = "SampleType")

# List of SE objects is returned. 
se_list
#> List of length 9
#> names(9): Soil Feces Skin Tongue ... Ocean Sediment (estuary) Mock

# Create arbitrary groups
rowData(tse)$group <- sample(1:3, nrow(tse), replace = TRUE)
colData(tse)$group <- sample(1:3, ncol(tse), replace = TRUE)

# Split based on rows
# Each element is named based on their group name. If you don't want to name
# elements, use use_name = FALSE. Since "group" can be found from rowdata and
# colData you must use `by`.
se_list <- splitOn(tse, group = "group", use.names = FALSE, by = 1)

# When column names are shared between elements, you can store the list to
# altExps
altExps(tse) <- se_list
#> Warning: 'names(value)' is NULL, replacing with 'unnamed'

altExps(tse)
#> List of length 3
#> names(3): unnamed1 unnamed2 unnamed3

# If you want to split on columns and update rowTree, you can do
se_list <- splitOn(tse, group = colData(tse)$group, update.tree = TRUE)

# If you want to combine groups back together, you can use unsplitBy
unsplitOn(se_list)
#> class: TreeSummarizedExperiment 
#> dim: 19216 26 
#> metadata(0):
#> assays(1): counts
#> rownames(19216): 549322 522457 ... 200359 271582
#> rowData names(8): Kingdom Phylum ... Species group
#> colnames(26): CL3 M11Fcsw ... NP2 TS28
#> colData names(8): X.SampleID Primer ... Description group
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: a LinkDataFrame (19216 rows)
#> rowTree: 1 phylo tree(s) (19216 leaves)
#> colLinks: NULL
#> colTree: NULL