rliger (version 1.0.0)

normalize: 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

# NOT RUN {
# Demonstration using matrices with randomly generated numbers
Y <- matrix(runif(5000,0,2), 10,500)
Z <- matrix(runif(5000,0,2), 10,500)
ligerex <- createLiger(list(y_set = Y, z_set = Z))
ligerex <- normalize(ligerex)
# }