updateLigerObject: Update old liger object to up-to-date structure

In rliger: Linked Inference of Genomic Experimental Relationships

Update old liger object to up-to-date structure

Description

Due to massive updates since rliger 2.0, old liger object structures are no longer compatible with the current package. This function will update the object to the latest structure.

Usage

updateLigerObject(
  object,
  dimredName,
  clusterName = "clusters",
  h5FilePath = NULL
)

Arguments

object	An object of any version of rliger
dimredName	Name of the dimension reduction embedding to be stored. Please see Details section.
clusterName	Name of the clustering assignment variable to be stored. Please see Details section.
h5FilePath	Named character vector for all H5 file paths. Not required for object run with in-memory analysis. For object containing H5-based analysis (e.g. online iNMF), this must be supplied if the H5 file location is different from that at creation time.

Details

Old liger object (<1.99.0) stores only one embedding at slot tsne.coords. dimredName must be specified as a single character. Pre-release version (1.99.0) stores multiple embeddings in cellMeta. dimredName must be exact existing variable names in cellMeta slot.

Old liger object stores clustering assignment in slot clusters. clusterName must be specified as a single character. Pre-release version does not require this.

Value

Updated liger object.

Examples

## Not run: 
# Suppose you have a liger object of old version (<1.99.0)
newLig <- updateLigerObject(oldLig,
                            dimredName = "UMAP",
                            clusterName = "louvain")

## End(Not run)

rliger documentation built on Oct. 30, 2024, 1:07 a.m.