TOAST-NMF deconvolution

The function runs TOAST iteratively with NMF to find compartment proportions and signatures

csDeCompress(
  Y_raw,
  K,
  nMarker = 1000,
  FUN = nmfOut,
  InitMarker = NULL,
  TotalIter = 30,
  bound_negative = FALSE
)

Arguments

Y_raw

matrix, numeric expression matrix
K

integer, number of cell-types
nMarker

integer, max number of genes for deconv, default 1000
FUN

function, defaults to nmfOut
InitMarker

vector, initial marker vector smaller than nrow of Y_raw
bound_negative

logical, T/F to bound negative params at 0

Value

list with cell-type proportions and expression profiles