rliger: subsetLiger – R documentation

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subsetLiger

Construct a liger object with a specified subset

Description

The subset can be based on cell names or clusters. This function applies the subsetting to raw.data, norm.data, scale.data, cell.data, H, W, V, H.norm, tsne.coords, and clusters. Note that it does NOT reoptimize the factorization. See optimizeSubset for this functionality.

Usage

subsetLiger(
  object,
  clusters.use = NULL,
  cells.use = NULL,
  remove.missing = TRUE
)

Arguments

`object`	`liger` object. Should run quantileAlignSNF and runTSNE before calling.
`clusters.use`	Clusters to use for subset.
`cells.use`	Vector of cell names to keep from any dataset.
`remove.missing`	Whether to remove genes/cells with no expression when creating new object (default TRUE).

Value

liger object with subsetting applied to raw.data, norm.data, scale.data, H, W, V, H.norm, tsne.coords, and clusters.

Examples

## Not run: 
# ligerex (liger object based on in-memory datasets), with clusters 0:10
# factorization, alignment, and t-SNE calculation have been performed
# subset by clusters
ligerex_subset <- subsetLiger(ligerex, clusters.use = c(1, 4, 5))

## End(Not run)

rliger

Linked Inference of Genomic Experimental Relationships

v1.0.0

GPL-3

Authors

Joshua Welch [aut, ctb], Chao Gao [aut, ctb, cre], Jialin Liu [aut, ctb], Joshua Sodicoff [aut, ctb], Velina Kozareva [aut, ctb], Evan Macosko [aut, ctb], Paul Hoffman [ctb], Ilya Korsunsky [ctb], Robert Lee [ctb]

Initial release

2021-04-18