iterateSigs: Use NMF repeatedly with TOAST framework to find cell-type...

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

Description

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

Usage

iterateSigs(
  yref,
  n.types = NULL,
  n.markers = 1000,
  n.iter = 30,
  scree = c("drop", "cumvar", "residual"),
  logTransform = F
)

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
iters	numeric, number of interations
pval	numeric, p-value cutoff
log	logical, T/F if yref is in log-scale

Value

list with cell-type proportions and expression profiles

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