splitOn: Split 'TreeSummarizedExperiment' column-wise or row-wise...
In microbiome/mia: Microbiome analysis

splitOn

R Documentation

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

Description

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

Usage

splitOn(x, ...)

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

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

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

unsplitOn(x, ...)

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

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

## S4 method for signature '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`)
`f`	`Character vector`. Specifies the grouping variable from `rowData` or `colData` or a `factor` or `vector` with the same length as one of the dimensions. If `f` matches with both dimensions, `by` must be specified. Split by cols is not encouraged, since this is not compatible with storing the results in `altExps`. (Default: `NULL`)
`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.

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.

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.

Author(s)

Leo Lahti and Tuomas Borman. Contact: microbiome.github.io

Examples

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

# List of SE objects is returned. 
se_list

# 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, f = "group", use.names = FALSE, by = 1)

# When column names are shared between elements, you can store the list to altExps
altExps(tse) <- se_list

altExps(tse)

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

# If you want to combine groups back together, you can use unsplitBy
unsplitOn(se_list)

microbiome/mia documentation built on Aug. 14, 2024, 4:42 p.m.