rliger (version 2.2.0)

updateLigerObject: 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
)

Value

Updated liger object.

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.

Examples

if (FALSE) {
# Suppose you have a liger object of old version (<1.99.0)
newLig <- updateLigerObject(oldLig,
                            dimredName = "UMAP",
                            clusterName = "louvain")
}