rliger: ligerToSeurat – R documentation

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ligerToSeurat

Create a Seurat object containing the data from a liger object

Description

Merges raw.data and scale.data of object, and creates Seurat object with these values along with tsne.coords, iNMF factorization, and cluster assignments. Supports Seurat V2 and V3.

Usage

ligerToSeurat(
  object,
  nms = names(object@H),
  renormalize = TRUE,
  use.liger.genes = TRUE,
  by.dataset = FALSE
)

Arguments

`object`	`liger` object.
`nms`	By default, labels cell names with dataset of origin (this is to account for cells in different datasets which may have same name). Other names can be passed here as vector, must have same length as the number of datasets. (default names(H))
`renormalize`	Whether to log-normalize raw data using Seurat defaults (default TRUE).
`use.liger.genes`	Whether to carry over variable genes (default TRUE).
`by.dataset`	Include dataset of origin in cluster identity in Seurat object (default FALSE).

Details

Stores original dataset identity by default in new object metadata if dataset names are passed in nms. iNMF factorization is stored in dim.reduction object with key "iNMF".

Value

Seurat object with raw.data, scale.data, dr$tsne, dr$inmf, and ident slots set.

Examples

## Not run: 
# ligerex (liger object based on in-memory datasets ONLY), factorization complete input
s.object <- ligerToSeurat(ligerex)

## 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