Use NMF repeatedly with TOAST framework to find cell-type gene signatures and do deconvolution

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

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