rliger (version 1.0.0)

scaleNotCenter: Scale genes by root-mean-square across cells

Description

This function scales normalized gene expression data after variable genes have been selected. Note that the data is not mean-centered before scaling because expression values must remain positive (NMF only accepts positive values). It also removes cells which do not have any expression across the genes selected, by default.

Usage

scaleNotCenter(object, remove.missing = TRUE, chunk = 1000, verbose = TRUE)

Arguments

object

liger object. Should call normalize and selectGenes before calling.

remove.missing

Whether to remove cells from scale.data with no gene expression (default TRUE).

chunk

size of chunks in hdf5 file. (default 1000)

verbose

Print progress bar/messages (TRUE by default)

Value

liger object with scale.data slot set.

Examples

# NOT RUN {
# Given datasets Y and Z
ligerex <- createLiger(list(y_set = Y, z_set = Z))
ligerex <- normalize(ligerex)
# use default selectGenes settings (var.thresh = 0.1)
ligerex <- selectGenes(ligerex)
ligerex <- scaleNotCenter(ligerex)
# }