Find cell-type gene signatures and do deconvolution — bestDeconvolution • DeCompress

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