Subset_LIGER: Subset LIGER object

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Subset LIGER object

Description

Subset LIGER object by cluster or other meta data variable.

Usage

Subset_LIGER(
  liger_object,
  cluster = NULL,
  cluster_col = "leiden_cluster",
  ident = NULL,
  ident_col = NULL,
  invert = FALSE
)

Arguments

liger_object	LIGER object name.
cluster	Name(s) of cluster to subset from object.
cluster_col	name of ⁠@cellMeta⁠ column containing cluster names, default is "leiden_cluster".
ident	variable within ident_col to use in sub-setting object.
ident_col	column in ⁠@cellMeta⁠ that contains values provided to ident.
invert	logical, whether to subset the inverse of the clusters or idents provided, default is FALSE.

Value

liger object

Examples

## Not run: 
# subset clusters 3 and 5
sub_liger <- subset_liger(liger_object = liger_object, cluster = c(3, 5))

# subset control samples from column "Treatment"
sub_liger <- subset_liger(liger_object = liger_object, ident = "control",
ident_col = "Treatment")

# subset control samples from column "Treatment" in clusters 3 and 5
sub_liger <- subset_liger(liger_object = liger_object, ident = "control",
ident_col = "Treatment", cluster = c(3, 5))

# Remove cluster 9
sub_liger <- subset_liger(liger_object = liger_object, cluster = 9, invert = TRUE)

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.