preprocess_for_transfer: Preprocess expression matrix as input for data transfer

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

Description

Subset to the shared gene sets between target data and reference factor matrix. Depth normalized, log transform, scale but not centered

Usage

preprocess_for_transfer(
  counts,
  Wref,
  scale.factor = 10000,
  scale = T,
  center = F,
  verbose = F
)

Arguments

counts	ncells-by-ngenes raw count matrix from target data
Wref	ngenes-by-r reference factor matrix
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 scalar, whether to show extensive program logs (default TRUE)

Value

A list containing

exprs

ncell-by-ngenes preprocessed expresssion matrix

Wref

ngenes-by-r reference factor matrix, with genes filtered

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