csDeCompress: TOAST-NMF deconvolution

In bhattacharya-a-bt/DeCompress: Tissue compartment deconvolution for targeted RNA panels

Description

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

Usage

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

bhattacharya-a-bt/DeCompress documentation built on March 28, 2021, 3:52 a.m.