Find cell-type gene signatures and do deconvolution

The function finds cell-type gene signatures and does deconvolution using the TOAST framework with NMF

bestDeconvolution(
  yref,
  n.types = NULL,
  scree = "drop",
  logTransform = F,
  known.props = NULL,
  methods = c("TOAST", "linseed", "celldistinguisher")
)

Arguments

yref

matrix, numeric expression matrix
n.types

integer, number of cell-types
scree

character, method to estimate n.types if n.types is NULL
logTransform

logical, T/F if yref is in log-scale
known.props

matrix, known proportion matrix, NULL if not known
methods

vector, character vector of deconv methods to use

Value

list with cell-type proportions and expression profiles