normalize: Normalize raw datasets to column sums

In rliger: Linked Inference of Genomic Experimental Relationships

Normalize raw datasets to column sums

Description

This function normalizes data to account for total gene expression across a cell.

Usage

normalize(
  object,
  chunk = 1000,
  format.type = "10X",
  remove.missing = TRUE,
  verbose = TRUE
)

Arguments

object	liger object.
chunk	size of chunks in hdf5 file. (default 1000)
format.type	string of HDF5 format (10X CellRanger by default).
remove.missing	Whether to remove cells not expressing any measured genes, and genes not expressed in any cells (if take.gene.union = TRUE, removes only genes not expressed in any dataset) (default TRUE).
verbose	Print progress bar/messages (TRUE by default)

Value

liger object with norm.data slot set.

Examples

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
ligerex <- normalize(ligerex)

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