reorganizeLiger: Construct a liger object organized by another feature
In rliger: Linked Inference of Genomic Experimental Relationships

reorganizeLiger

R Documentation

Construct a liger object organized by another feature

Description

Using the same data, rearrange functional datasets using another discrete feature in cell.data. This removes most computed data slots, though cell.data and current clustering can be retained.

Usage

reorganizeLiger(
  object,
  by.feature,
  keep.meta = TRUE,
  new.label = "orig.dataset",
  ...
)

Arguments

`object`	`liger` object.
`by.feature`	Column in cell.data to use in reorganizing raw data.
`keep.meta`	Whether to carry over all existing data in cell.data slot (default TRUE).
`new.label`	If cell.data is to be retained, new column name for original organizing feature (previously labeled as dataset) (default "orig.dataset")
`...`	Additional parameters passed on to createLiger.

Value

liger object with rearranged raw.data slot.

Examples

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
# Create a random variable of two categories
ligerex@cell.data$foo <- factor(sample(c(1,2), 600, replace = TRUE))
ligerexFoo <- reorganizeLiger(ligerex, "foo")

rliger documentation built on Nov. 9, 2023, 1:07 a.m.