preprocess_for_integration: Preprocess expression matrix as input for data integration

In pengminshi/cFIT: cFIT (common Factor Space Integration & Transfer)

Description

Preprocess, leave highly expressed genes, depth normalized, log transform, scale but not centered

Usage

preprocess_for_integration(
  X.list,
  genes,
  scale.factor = 10000,
  scale = T,
  center = F,
  verbose = F
)

Arguments

X.list	A list of m ncells-by-ngenes, gene expression matrices from m data sets
genes	character vector, a vector of gene names (selected highly variable genes)
scale.factor	scalar, scaling factor for library size normalization (default 1e4)
scale	boolean, whether to scale per gene expression (default TRUE)
center	boolean, whether to center per gene expression (default FALSE)
verbose	boolean, whether to show messages

Value

preprocessed expression list X.list

pengminshi/cFIT documentation built on July 11, 2021, 11:12 p.m.